id string | task_type string | pipeline string | difficulty string | num_hops int64 | question string | context string | reasoning_chain dict | answer string | choices list | modalities list | modality_data list | evidence list | metadata unknown | path_confidence_score float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
co_path_00100 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ALK to PMS2 through known protein interactions and pathway memberships? | ALK GENE_ANNOTATED_WITH_GO_TERM ATP binding -> PMS2 GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ALK",
"source_node_type": "GENE",
"source_node_label": "ALK",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id"... | ALK -> ATP binding -> PMS2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALK",
"source_db": "UniProt",
"payload": {
"accession": "Q9UM73",
"sequence": "MGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPLSYSRLQRKSLAVDFVVPSLFRVYARDLLLPPSSSELKAGRPEARGSLALDCAPLLRLLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKL... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "ALK GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "PMS2",
"text": "PMS2 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
}
] | {
"gene_a": "ALK",
"gene_b": "PMS2",
"path_length": 2
} | 0.6 |
co_path_00101 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from SQSTM1 to CD4 through known protein interactions and pathway memberships? | SQSTM1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> CD4 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding | {
"steps": [
{
"hop": 1,
"source_node_id": "SQSTM1",
"source_node_type": "GENE",
"source_node_label": "SQSTM1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_... | SQSTM1 -> protein kinase binding -> CD4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SQSTM1",
"source_db": "UniProt",
"payload": {
"accession": "Q13501",
"sequence": "MASLTVKAYLLGKEDAAREIRRFSFCCSPEPEAEAEAAAGPGPCERLLSRVAALFPALRPGGFQAHYRDEDGDLVAFSSDEELTMAMSYVKDDIFRIYIKEKKECRRDHRPPCAQEAPRNMVHPNVICDGCN... | [
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "SQSTM1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CD4",
"text": "CD4 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
}
] | {
"gene_a": "SQSTM1",
"gene_b": "CD4",
"path_length": 2
} | 0.6 |
co_path_00102 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from VCP to CASP3 through known protein interactions and pathway memberships? | VCP GENE_PARTICIPATES_IN_PATHWAY Neddylation -> CDKN1A GENE_PARTICIPATES_IN_PATHWAY Neddylation -> CASP3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDKN1A | {
"steps": [
{
"hop": 1,
"source_node_id": "VCP",
"source_node_type": "GENE",
"source_node_label": "VCP",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_id": "R... | VCP -> Neddylation -> CDKN1A -> CASP3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "VCP",
"source_db": "UniProt",
"payload": {
"accession": "P55072",
"sequence": "MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-8951664",
"text": "VCP GENE_PARTICIPATES_IN_PATHWAY Neddylation",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "CDKN1A",
"text": "CDKN1A GENE_PARTICIPATES_IN_PATHWAY Neddylation",
"confidence": 1
},
{
"source_db... | {
"gene_a": "VCP",
"gene_b": "CASP3",
"path_length": 3
} | 0.998665 |
co_path_00103 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from MLH3 to VPS35 through known protein interactions and pathway memberships? | MLH3 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ATP13A2 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ATP13A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH VPS35 | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH3",
"source_node_type": "GENE",
"source_node_label": "MLH3",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:InterPro",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": ... | MLH3 -> ATP binding -> ATP13A2 -> VPS35 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH3",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHC1",
"sequence": "MIKCLSVEVQAKLRSGLAISSLGQCVEELALNSIDAEAKCVAVRVNMETFQVQVIDNGFGMGSDDVEKVGNRYFTSKCHSVQDLENPRFYGFRGEALANIADMASAVEISSKKNRTMKTFVKLFQSGKALKACE... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "MLH3 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ATP13A2",
"text": "ATP13A2 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "STRING... | {
"gene_a": "MLH3",
"gene_b": "VPS35",
"path_length": 3
} | 0.675448 |
co_path_00104 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from BDNF to VPS35 through known protein interactions and pathway memberships? | BDNF GENE_ANNOTATED_WITH_GO_TERM modulation of chemical synaptic transmission -> VPS35 GENE_ANNOTATED_WITH_GO_TERM modulation of chemical synaptic transmission | {
"steps": [
{
"hop": 1,
"source_node_id": "BDNF",
"source_node_type": "GENE",
"source_node_label": "BDNF",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IBA:GO_Central",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id"... | BDNF -> modulation of chemical synaptic transmission -> VPS35 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BDNF",
"source_db": "UniProt",
"payload": {
"accession": "P23560",
"sequence": "MTILFLTMVISYFGCMKAAPMKEANIRGQGGLAYPGVRTHGTLESVNGPKAGSRGLTSLADTFEHVIEELLDEDQKVRPNEENNKDADLYTSRVMLSSQVPLEPPLLFLLEEYKNYLDAANMSMRVRRHSDPAR... | [
{
"source_db": "GO",
"source_id": "GO:0050804",
"text": "BDNF GENE_ANNOTATED_WITH_GO_TERM modulation of chemical synaptic transmission",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "VPS35",
"text": "VPS35 GENE_ANNOTATED_WITH_GO_TERM modulation of chemical synaptic transmis... | {
"gene_a": "BDNF",
"gene_b": "VPS35",
"path_length": 2
} | 0.6 |
co_path_00105 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from ACKR3 to BCOR through known protein interactions and pathway memberships? | Single allele VARIANT_IN_GENE ACKR3 -> Single allele VARIANT_IN_GENE MYC -> MYC GENE_ANNOTATED_WITH_GO_TERM DNA-binding transcription factor binding -> BCOR GENE_ANNOTATED_WITH_GO_TERM DNA-binding transcription factor binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ACKR3",
"source_node_type": "GENE",
"source_node_label": "ACKR3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | ACKR3 -> Single allele -> MYC -> DNA-binding transcription factor binding -> BCOR | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACKR3",
"source_db": "UniProt",
"payload": {
"accession": "P25106",
"sequence": "MDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIGMIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCKVTHLIFSINLFGSIF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACKR3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MYC",
"text": "Single allele VARIANT_IN_GENE MYC",
"confidence": 1
},
{
"source_db": "GO",
"source_id": "G... | {
"gene_a": "ACKR3",
"gene_b": "BCOR",
"path_length": 4
} | 0.774597 |
co_path_00106 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from KLK3 to CD2AP through known protein interactions and pathway memberships? | KLK3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AR -> AR GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> CBL GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> CD2AP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CBL | {
"steps": [
{
"hop": 1,
"source_node_id": "KLK3",
"source_node_type": "GENE",
"source_node_label": "KLK3",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.995,
"edge_source_db": "STRING",
"t... | KLK3 -> AR -> zinc ion binding -> CBL -> CD2AP | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KLK3",
"source_db": "UniProt",
"payload": {
"accession": "P07288",
"sequence": "MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTD... | [
{
"source_db": "STRING",
"source_id": "AR",
"text": "KLK3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AR",
"confidence": 0.995
},
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "AR GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
... | {
"gene_a": "KLK3",
"gene_b": "CD2AP",
"path_length": 4
} | 0.771295 |
co_path_00107 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from SLC6A2 to ACKR3 through known protein interactions and pathway memberships? | SLC6A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADRA2A -> ADRA2A GENE_PARTICIPATES_IN_PATHWAY G alpha (i) signalling events -> ACKR3 GENE_PARTICIPATES_IN_PATHWAY G alpha (i) signalling events | {
"steps": [
{
"hop": 1,
"source_node_id": "SLC6A2",
"source_node_type": "GENE",
"source_node_label": "SLC6A2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.802,
"edge_source_db": "STRING",
... | SLC6A2 -> ADRA2A -> G alpha (i) signalling events -> ACKR3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SLC6A2",
"source_db": "UniProt",
"payload": {
"accession": "P23975",
"sequence": "MLLARMNPQVQPENNGADTGPEQPLRARKTAELLVVKERNGVQCLLAPRDGDAQPRETWGKKIDFLLSVVGFAVDLANVWRFPYLCYKNGGGAFLIPYTLFLIIAGMPLFYMELALGQYNREGAATVWKICP... | [
{
"source_db": "STRING",
"source_id": "ADRA2A",
"text": "SLC6A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADRA2A",
"confidence": 0.802
},
{
"source_db": "Reactome",
"source_id": "R-HSA-418594",
"text": "ADRA2A GENE_PARTICIPATES_IN_PATHWAY G alpha (i) signalling events",
"confidence": ... | {
"gene_a": "SLC6A2",
"gene_b": "ACKR3",
"path_length": 3
} | 0.929091 |
co_path_00108 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ERBB2 to CAMK4 through known protein interactions and pathway memberships? | ERBB2 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> CAMK4 GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ERBB2",
"source_node_type": "GENE",
"source_node_label": "ERBB2",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node... | ERBB2 -> ATP binding -> CAMK4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERBB2",
"source_db": "UniProt",
"payload": {
"accession": "P04626",
"sequence": "MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGAS... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "ERBB2 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CAMK4",
"text": "CAMK4 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
}
] | {
"gene_a": "ERBB2",
"gene_b": "CAMK4",
"path_length": 2
} | 0.6 |
co_path_00109 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from FBXO7 to CD44 through known protein interactions and pathway memberships? | FBXO7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PARK7 -> PARK7 GENE_ANNOTATED_WITH_GO_TERM inflammatory response -> CD44 GENE_ANNOTATED_WITH_GO_TERM inflammatory response | {
"steps": [
{
"hop": 1,
"source_node_id": "FBXO7",
"source_node_type": "GENE",
"source_node_label": "FBXO7",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.864,
"edge_source_db": "STRING",
... | FBXO7 -> PARK7 -> inflammatory response -> CD44 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FBXO7",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y3I1",
"sequence": "MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPAPNIPSSTDSEHSSLQNNEQPSLATSSNQTSMQDEQPSDSFQGQAAQSGV... | [
{
"source_db": "STRING",
"source_id": "PARK7",
"text": "FBXO7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PARK7",
"confidence": 0.864
},
{
"source_db": "GO",
"source_id": "GO:0006954",
"text": "PARK7 GENE_ANNOTATED_WITH_GO_TERM inflammatory response",
"confidence": 0.6
},
{
"sou... | {
"gene_a": "FBXO7",
"gene_b": "CD44",
"path_length": 3
} | 0.677546 |
co_path_00110 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from BAX to ABCA7 through known protein interactions and pathway memberships? | BAX GENE_ANNOTATED_WITH_GO_TERM positive regulation of apoptotic process -> BIN1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of apoptotic process -> ABCA7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BIN1 | {
"steps": [
{
"hop": 1,
"source_node_id": "BAX",
"source_node_type": "GENE",
"source_node_label": "BAX",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | BAX -> positive regulation of apoptotic process -> BIN1 -> ABCA7 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BAX",
"source_db": "UniProt",
"payload": {
"accession": "Q07812",
"sequence": "MDGSGEQPRGGGPTSSEQIMKTGALLLQGFIQDRAGRMGGEAPELALDPVPQDASTKKLSECLKRIGDELDSNMELQRMIAAVDTDSPREVFFRVAADMFSDGNFNWGRVVALFYFASKLVLKALCTKVPELIRT... | [
{
"source_db": "GO",
"source_id": "GO:0043065",
"text": "BAX GENE_ANNOTATED_WITH_GO_TERM positive regulation of apoptotic process",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BIN1",
"text": "BIN1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of apoptotic process",
... | {
"gene_a": "BAX",
"gene_b": "ABCA7",
"path_length": 3
} | 0.666924 |
co_path_00111 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from AURKA to AURKB through known protein interactions and pathway memberships? | AURKA PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BIRC5 -> BIRC5 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AURKB | {
"steps": [
{
"hop": 1,
"source_node_id": "AURKA",
"source_node_type": "GENE",
"source_node_label": "AURKA",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.993,
"edge_source_db": "STRING",
... | AURKA -> BIRC5 -> AURKB | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AURKA",
"source_db": "UniProt",
"payload": {
"accession": "O14965",
"sequence": "MDRSKENCISGPVKATAPVGGPKRVLVTQQFPCQNPLPVNSGQAQRVLCPSNSSQRIPLQAQKLVSSHKPVQNQKQKQLQATSVPHPVSRPLNNTQKSKQPLPSAPENNPEEELASKQKNEESKKRQWALEDF... | [
{
"source_db": "STRING",
"source_id": "BIRC5",
"text": "AURKA PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BIRC5",
"confidence": 0.993
},
{
"source_db": "STRING",
"source_id": "AURKB",
"text": "BIRC5 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AURKB",
"confidence": 0.999
}
] | {
"gene_a": "AURKA",
"gene_b": "AURKB",
"path_length": 2
} | 0.995995 |
co_path_00112 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from BRIP1 to AVPR1A through known protein interactions and pathway memberships? | BRIP1 GENE_PARTICIPATES_IN_PATHWAY HDR through Single Strand Annealing (SSA) -> ABL1 GENE_PARTICIPATES_IN_PATHWAY HDR through Single Strand Annealing (SSA) -> ABL1 GENE_ANNOTATED_WITH_GO_TERM protein kinase C binding -> AVPR1A GENE_ANNOTATED_WITH_GO_TERM protein kinase C binding | {
"steps": [
{
"hop": 1,
"source_node_id": "BRIP1",
"source_node_type": "GENE",
"source_node_label": "BRIP1",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_id"... | BRIP1 -> HDR through Single Strand Annealing (SSA) -> ABL1 -> protein kinase C binding -> AVPR1A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-5685938",
"text": "BRIP1 GENE_PARTICIPATES_IN_PATHWAY HDR through Single Strand Annealing (SSA)",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "ABL1",
"text": "ABL1 GENE_PARTICIPATES_IN_PATHWAY HDR through Single Strand Ann... | {
"gene_a": "BRIP1",
"gene_b": "AVPR1A",
"path_length": 4
} | 0.774597 |
co_path_00113 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from GRN to ATP6V1B2 through known protein interactions and pathway memberships? | GRN GENE_ANNOTATED_WITH_GO_TERM lysosomal lumen acidification -> ATP6V1A GENE_ANNOTATED_WITH_GO_TERM lysosomal lumen acidification -> ATP6V1A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ATP6V1B2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRN",
"source_node_type": "GENE",
"source_node_label": "GRN",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IMP:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | GRN -> lysosomal lumen acidification -> ATP6V1A -> ATP6V1B2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "GRN",
"source_db": "UniProt",
"payload": {
"accession": "P28799",
"sequence": "MWTLVSWVALTAGLVAGTRCPDGQFCPVACCLDPGGASYSCCRPLLDKWPTTLSRHLGGPCQVDAHCSAGHSCIFTVSGTSSCCPFPEAVACGDGHHCCPRGFHCSADGRSCFQRSGNNSVGAIQCPDSQFECPD... | [
{
"source_db": "GO",
"source_id": "GO:0007042",
"text": "GRN GENE_ANNOTATED_WITH_GO_TERM lysosomal lumen acidification",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ATP6V1A",
"text": "ATP6V1A GENE_ANNOTATED_WITH_GO_TERM lysosomal lumen acidification",
"confidence": 0.... | {
"gene_a": "GRN",
"gene_b": "ATP6V1B2",
"path_length": 3
} | 0.711141 |
co_path_00114 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from ATP6V1A to SPOP through known protein interactions and pathway memberships? | ATP6V1A GENE_ANNOTATED_WITH_GO_TERM ATP binding -> PIK3CA GENE_ANNOTATED_WITH_GO_TERM ATP binding -> PTEN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PIK3CA -> PTEN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SPOP | {
"steps": [
{
"hop": 1,
"source_node_id": "ATP6V1A",
"source_node_type": "GENE",
"source_node_label": "ATP6V1A",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_... | ATP6V1A -> ATP binding -> PIK3CA -> PTEN -> SPOP | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATP6V1A",
"source_db": "UniProt",
"payload": {
"accession": "P38606",
"sequence": "MDFSKLPKILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDI... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "ATP6V1A GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "PIK3CA",
"text": "PIK3CA GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "STRIN... | {
"gene_a": "ATP6V1A",
"gene_b": "SPOP",
"path_length": 4
} | 0.771685 |
co_path_00115 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from MAPK1 to BRCA1 through known protein interactions and pathway memberships? | MAPK1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53 -> BRCA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPK1",
"source_node_type": "GENE",
"source_node_label": "MAPK1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
... | MAPK1 -> TP53 -> BRCA1 | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPK1",
"source_db": "UniProt",
"payload": {
"accession": "P28482",
"sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQI... | [
{
"source_db": "STRING",
"source_id": "TP53",
"text": "MAPK1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53",
"confidence": 0.998
},
{
"source_db": "STRING",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53",
"confidence": 0.999
}
] | {
"gene_a": "MAPK1",
"gene_b": "BRCA1",
"path_length": 2
} | 0.9985 |
co_path_00116 | path_traversal | coding_variant | easy | 3 | What is the shortest molecular path from KLK3 to LRRK2 through known protein interactions and pathway memberships? | KLK3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AR -> AR PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1 -> LRRK2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "KLK3",
"source_node_type": "GENE",
"source_node_label": "KLK3",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.995,
"edge_source_db": "STRING",
"t... | KLK3 -> AR -> HSP90AA1 -> LRRK2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KLK3",
"source_db": "UniProt",
"payload": {
"accession": "P07288",
"sequence": "MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTD... | [
{
"source_db": "STRING",
"source_id": "AR",
"text": "KLK3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AR",
"confidence": 0.995
},
{
"source_db": "STRING",
"source_id": "HSP90AA1",
"text": "AR PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1",
"confidence": 0.999
},
{
"source_db": "... | {
"gene_a": "KLK3",
"gene_b": "LRRK2",
"path_length": 3
} | 0.987916 |
co_path_00117 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from MLH1 to SOD1 through known protein interactions and pathway memberships? | MLH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BLM -> BLM GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> SOD1 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH1",
"source_node_type": "GENE",
"source_node_label": "MLH1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | MLH1 -> BLM -> protein homodimerization activity -> SOD1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "STRING",
"source_id": "BLM",
"text": "MLH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BLM",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0042803",
"text": "BLM GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": 0.6
},
{
... | {
"gene_a": "MLH1",
"gene_b": "SOD1",
"path_length": 3
} | 0.711141 |
co_path_00118 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from CDK12 to ADRA2B through known protein interactions and pathway memberships? | CDK12 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> ADRA2A GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> ADRA2B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADRA2A | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK12",
"source_node_type": "GENE",
"source_node_label": "CDK12",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:Ensembl",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | CDK12 -> protein kinase binding -> ADRA2A -> ADRA2B | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK12",
"source_db": "UniProt",
"payload": {
"accession": "Q9NYV4",
"sequence": "MPNSERHGGKKDGSGGASGTLQPSSGGGSSNSRERHRLVSKHKRHKSKHSKDMGLVTPEAASLGTVIKPLVEYDDISSDSDTFSDDMAFKLDRRENDERRGSDRSDRLHKHRHHQHRRSRDLLKAKQTEKEKS... | [
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "CDK12 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ADRA2A",
"text": "ADRA2A GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
... | {
"gene_a": "CDK12",
"gene_b": "ADRA2B",
"path_length": 3
} | 0.618742 |
co_path_00119 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from ADRA2C to DCTN4 through known protein interactions and pathway memberships? | ADRA2C PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADRA2A -> ADRA2A GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> DCTN1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> DCTN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH DCTN4 | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2C",
"source_node_type": "GENE",
"source_node_label": "ADRA2C",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.781,
"edge_source_db": "STRING",
... | ADRA2C -> ADRA2A -> protein kinase binding -> DCTN1 -> DCTN4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2C",
"source_db": "UniProt",
"payload": {
"accession": "P18825",
"sequence": "MASPALAAALAVAAAAGPNASGAGERGSGGVANASGASWGPPRGQYSAGAVAGLAAVVGFLIVFTVVGNVLVVIAVLTSRALRAPQNLFLVSLASADILVATLVMPFSLANELMAYWYFGQVWCGVYLALDV... | [
{
"source_db": "STRING",
"source_id": "ADRA2A",
"text": "ADRA2C PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADRA2A",
"confidence": 0.781
},
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "ADRA2A GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
... | {
"gene_a": "ADRA2C",
"gene_b": "DCTN4",
"path_length": 4
} | 0.727997 |
co_path_00120 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from DCTN1 to AFP through known protein interactions and pathway memberships? | DCTN1 GENE_PARTICIPATES_IN_PATHWAY Processing of antigen in germinal center B cells -> TUBA4A GENE_PARTICIPATES_IN_PATHWAY Processing of antigen in germinal center B cells -> TUBA4A GENE_ANNOTATED_WITH_GO_TERM metal ion binding -> AFP GENE_ANNOTATED_WITH_GO_TERM metal ion binding | {
"steps": [
{
"hop": 1,
"source_node_id": "DCTN1",
"source_node_type": "GENE",
"source_node_label": "DCTN1",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_id"... | DCTN1 -> Processing of antigen in germinal center B cells -> TUBA4A -> metal ion binding -> AFP | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "DCTN1",
"source_db": "UniProt",
"payload": {
"accession": "Q14203",
"sequence": "MAQSKRHVYSRTPSGSRMSAEASARPLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGVILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVFEDGADTTSPETPDSSASKVLKREGTDTTAKTSKLRG... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-9979719",
"text": "DCTN1 GENE_PARTICIPATES_IN_PATHWAY Processing of antigen in germinal center B cells",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "TUBA4A",
"text": "TUBA4A GENE_PARTICIPATES_IN_PATHWAY Processing of anti... | {
"gene_a": "DCTN1",
"gene_b": "AFP",
"path_length": 4
} | 0.774597 |
co_path_00121 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from MYC to BCHE through known protein interactions and pathway memberships? | MYC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53 -> TP53 GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation -> BCHE GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.997,
"edge_source_db": "STRING",
"tar... | MYC -> TP53 -> negative regulation of cell population proliferation -> BCHE | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "STRING",
"source_id": "TP53",
"text": "MYC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53",
"confidence": 0.997
},
{
"source_db": "GO",
"source_id": "GO:0008285",
"text": "TP53 GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation",
"confiden... | {
"gene_a": "MYC",
"gene_b": "BCHE",
"path_length": 3
} | 0.710667 |
co_path_00122 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from PSEN1 to SETX through known protein interactions and pathway memberships? | PSEN1 GENE_ANNOTATED_WITH_GO_TERM DNA damage response -> SETX GENE_ANNOTATED_WITH_GO_TERM DNA damage response | {
"steps": [
{
"hop": 1,
"source_node_id": "PSEN1",
"source_node_type": "GENE",
"source_node_label": "PSEN1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:ARUK-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id"... | PSEN1 -> DNA damage response -> SETX | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PSEN1",
"source_db": "UniProt",
"payload": {
"accession": "P49768",
"sequence": "MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSRQVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTEDTETVGQRALHSI... | [
{
"source_db": "GO",
"source_id": "GO:0006974",
"text": "PSEN1 GENE_ANNOTATED_WITH_GO_TERM DNA damage response",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "SETX",
"text": "SETX GENE_ANNOTATED_WITH_GO_TERM DNA damage response",
"confidence": 0.6
}
] | {
"gene_a": "PSEN1",
"gene_b": "SETX",
"path_length": 2
} | 0.6 |
co_path_00123 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from AR to CHCHD10 through known protein interactions and pathway memberships? | AR PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1 -> LRRK2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1 -> LRRK2 GENE_ANNOTATED_WITH_GO_TERM mitochondrion organization -> CHCHD10 GENE_ANNOTATED_WITH_GO_TERM mitochondrion organization | {
"steps": [
{
"hop": 1,
"source_node_id": "AR",
"source_node_type": "GENE",
"source_node_label": "AR",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"targe... | AR -> HSP90AA1 -> LRRK2 -> mitochondrion organization -> CHCHD10 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "STRING",
"source_id": "HSP90AA1",
"text": "AR PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1",
"confidence": 0.999
},
{
"source_db": "STRING",
"source_id": "LRRK2",
"text": "LRRK2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1",
"confidence": 0.97
},
{
"sour... | {
"gene_a": "AR",
"gene_b": "CHCHD10",
"path_length": 4
} | 0.768528 |
co_path_00124 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from SPTLC2 to ERBB4 through known protein interactions and pathway memberships? | SPTLC2 GENE_PARTICIPATES_IN_PATHWAY Sphingolipid de novo biosynthesis -> VAPB GENE_PARTICIPATES_IN_PATHWAY Sphingolipid de novo biosynthesis -> VAPB GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> ERBB4 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity | {
"steps": [
{
"hop": 1,
"source_node_id": "SPTLC2",
"source_node_type": "GENE",
"source_node_label": "SPTLC2",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_i... | SPTLC2 -> Sphingolipid de novo biosynthesis -> VAPB -> protein homodimerization activity -> ERBB4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SPTLC2",
"source_db": "UniProt",
"payload": {
"accession": "O15270",
"sequence": "MRPEPGGCCCRRTVRANGCVANGEVRNGYVRSSAAAAAAAAAGQIHHVTQNGGLYKRPFNEAFEETPMLVAVLTYVGYGVLTLFGYLRDFLRYWRIEKCHHATEREEQKDFVSLYQDFENFYTRNLYMRIRD... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-1660661",
"text": "SPTLC2 GENE_PARTICIPATES_IN_PATHWAY Sphingolipid de novo biosynthesis",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "VAPB",
"text": "VAPB GENE_PARTICIPATES_IN_PATHWAY Sphingolipid de novo biosynthesis",
... | {
"gene_a": "SPTLC2",
"gene_b": "ERBB4",
"path_length": 4
} | 0.774597 |
co_path_00125 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from MET to GRN through known protein interactions and pathway memberships? | MET PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HGF -> HGF GENE_ANNOTATED_WITH_GO_TERM growth factor activity -> GRN GENE_ANNOTATED_WITH_GO_TERM growth factor activity | {
"steps": [
{
"hop": 1,
"source_node_id": "MET",
"source_node_type": "GENE",
"source_node_label": "MET",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"tar... | MET -> HGF -> growth factor activity -> GRN | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MET",
"source_db": "UniProt",
"payload": {
"accession": "P08581",
"sequence": "MKAPAVLAPGILVLLFTLVQRSNGECKEALAKSEMNVNMKYQLPNFTAETPIQNVILHEHHIFLGATNYIYVLNEEDLQKVAEYKTGPVLEHPDCFPCQDCSSKANLSGGVWKDNINMALVVDTYYDDQLISCGS... | [
{
"source_db": "STRING",
"source_id": "HGF",
"text": "MET PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HGF",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0008083",
"text": "HGF GENE_ANNOTATED_WITH_GO_TERM growth factor activity",
"confidence": 0.6
},
{
"source_db"... | {
"gene_a": "MET",
"gene_b": "GRN",
"path_length": 3
} | 0.711141 |
co_path_00126 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from SYNJ1 to CCND1 through known protein interactions and pathway memberships? | SYNJ1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BIN1 -> BIN1 GENE_ANNOTATED_WITH_GO_TERM negative regulation of transcription by RNA polymerase II -> CCND1 GENE_ANNOTATED_WITH_GO_TERM negative regulation of transcription by RNA polymerase II | {
"steps": [
{
"hop": 1,
"source_node_id": "SYNJ1",
"source_node_type": "GENE",
"source_node_label": "SYNJ1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.994,
"edge_source_db": "STRING",
... | SYNJ1 -> BIN1 -> negative regulation of transcription by RNA polymerase II -> CCND1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SYNJ1",
"source_db": "UniProt",
"payload": {
"accession": "O43426",
"sequence": "MAFSKGFRIYHKLDPPPFSLIVETRHKEECLMFESGAVAVLSSAEKEAIKGTYSKVLDAYGLLGVLRLNLGDTMLHYLVLVTGCMSVGKIQESEVFRVTSTEFISLRIDSSDEDRISEVRKVLNSGNFYFAWS... | [
{
"source_db": "STRING",
"source_id": "BIN1",
"text": "SYNJ1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BIN1",
"confidence": 0.994
},
{
"source_db": "GO",
"source_id": "GO:0000122",
"text": "BIN1 GENE_ANNOTATED_WITH_GO_TERM negative regulation of transcription by RNA polymerase II",
"c... | {
"gene_a": "SYNJ1",
"gene_b": "CCND1",
"path_length": 3
} | 0.709953 |
co_path_00127 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from APH1B to LEPR through known protein interactions and pathway memberships? | APH1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APP -> Single allele VARIANT_IN_GENE APP -> Single allele VARIANT_IN_GENE LEPR | {
"steps": [
{
"hop": 1,
"source_node_id": "APH1B",
"source_node_type": "GENE",
"source_node_label": "APH1B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.866,
"edge_source_db": "STRING",
... | APH1B -> APP -> Single allele -> LEPR | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APH1B",
"source_db": "UniProt",
"payload": {
"accession": "Q8WW43",
"sequence": "MTAAVFFGCAFIAFGPALALYVFTIATEPLRIIFLIAGAFFWLVSLLISSLVWFMARVIIDNKDGPTQKYLLIFGAFVSVYIQEMFRFAYYKLLKKASEGLKSINPGETAPSMRLLAYVSGLGFGIMSGVFSF... | [
{
"source_db": "STRING",
"source_id": "APP",
"text": "APH1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APP",
"confidence": 0.866
},
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APP",
"confidence": 1
},
{
"source_db": "ClinVar",
... | {
"gene_a": "APH1B",
"gene_b": "LEPR",
"path_length": 3
} | 0.953175 |
co_path_00128 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from APP to CBL through known protein interactions and pathway memberships? | APP GENE_ANNOTATED_WITH_GO_TERM cellular response to nerve growth factor stimulus -> CBL GENE_ANNOTATED_WITH_GO_TERM cellular response to nerve growth factor stimulus | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:Ensembl",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "GO... | APP -> cellular response to nerve growth factor stimulus -> CBL | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "GO",
"source_id": "GO:1990090",
"text": "APP GENE_ANNOTATED_WITH_GO_TERM cellular response to nerve growth factor stimulus",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CBL",
"text": "CBL GENE_ANNOTATED_WITH_GO_TERM cellular response to nerve growth factor... | {
"gene_a": "APP",
"gene_b": "CBL",
"path_length": 2
} | 0.6 |
co_path_00129 | path_traversal | coding_variant | easy | 3 | What is the shortest molecular path from CD2AP to ESR1 through known protein interactions and pathway memberships? | CD2AP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CBL -> CBL PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SRC -> ESR1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SRC | {
"steps": [
{
"hop": 1,
"source_node_id": "CD2AP",
"source_node_type": "GENE",
"source_node_label": "CD2AP",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.988,
"edge_source_db": "STRING",
... | CD2AP -> CBL -> SRC -> ESR1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD2AP",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y5K6",
"sequence": "MVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKRETEFKDDSLPIKRERHGNVASLVQRISTYGLPAGGIQPHPQTKNIKKKTKKRQCKVLFEYIPQNEDELELKVGD... | [
{
"source_db": "STRING",
"source_id": "CBL",
"text": "CD2AP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CBL",
"confidence": 0.988
},
{
"source_db": "STRING",
"source_id": "SRC",
"text": "CBL PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SRC",
"confidence": 0.999
},
{
"source_db": "STRING... | {
"gene_a": "CD2AP",
"gene_b": "ESR1",
"path_length": 3
} | 0.99532 |
co_path_00130 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from ALS2 to AKAP11 through known protein interactions and pathway memberships? | ALS2 GENE_ANNOTATED_WITH_GO_TERM protein homooligomerization -> MAPT GENE_ANNOTATED_WITH_GO_TERM protein homooligomerization -> MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GSK3B -> AKAP11 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GSK3B | {
"steps": [
{
"hop": 1,
"source_node_id": "ALS2",
"source_node_type": "GENE",
"source_node_label": "ALS2",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:MGI",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "GO:0... | ALS2 -> protein homooligomerization -> MAPT -> GSK3B -> AKAP11 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALS2",
"source_db": "UniProt",
"payload": {
"accession": "Q96Q42",
"sequence": "MDSKKRSSTEAEGSKERGLVHIWQAGSFPITPERLPGWGGKTVLQAALGVKHGVLLTEDGEVYSFGTLPWRSGPVEICPSSPILENALVGQYVITVATGSFHSGAVTDNGVAYMWGENSAGQCAVANQQYVPEP... | [
{
"source_db": "GO",
"source_id": "GO:0051260",
"text": "ALS2 GENE_ANNOTATED_WITH_GO_TERM protein homooligomerization",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "MAPT",
"text": "MAPT GENE_ANNOTATED_WITH_GO_TERM protein homooligomerization",
"confidence": 0.6
},
... | {
"gene_a": "ALS2",
"gene_b": "AKAP11",
"path_length": 4
} | 0.74357 |
co_path_00131 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ATM to FUS through known protein interactions and pathway memberships? | ATM GENE_ANNOTATED_WITH_GO_TERM regulation of apoptotic process -> TARDBP GENE_ANNOTATED_WITH_GO_TERM regulation of apoptotic process -> TARDBP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FUS | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:Reactome",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "G... | ATM -> regulation of apoptotic process -> TARDBP -> FUS | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "GO",
"source_id": "GO:0042981",
"text": "ATM GENE_ANNOTATED_WITH_GO_TERM regulation of apoptotic process",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "TARDBP",
"text": "TARDBP GENE_ANNOTATED_WITH_GO_TERM regulation of apoptotic process",
"confidence": ... | {
"gene_a": "ATM",
"gene_b": "FUS",
"path_length": 3
} | 0.711141 |
co_path_00132 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ERG to ATP13A2 through known protein interactions and pathway memberships? | ERG PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AR -> AR GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> ATP13A2 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ERG",
"source_node_type": "GENE",
"source_node_label": "ERG",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.893,
"edge_source_db": "STRING",
"tar... | ERG -> AR -> zinc ion binding -> ATP13A2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERG",
"source_db": "UniProt",
"payload": {
"accession": "P11308",
"sequence": "MASTIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPDECSVAKGGKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWS... | [
{
"source_db": "STRING",
"source_id": "AR",
"text": "ERG PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AR",
"confidence": 0.893
},
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "AR GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
... | {
"gene_a": "ERG",
"gene_b": "ATP13A2",
"path_length": 3
} | 0.685043 |
co_path_00133 | path_traversal | coding_variant | hard | 5 | What is the shortest molecular path from ATXN2 to MALAT1 through known protein interactions and pathway memberships? | ATXN2 PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex -> ILF3 PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex -> ILF3 GENE_ENCODES_PROTEIN ILF3 -> ILF3 PROTEIN_PHYSICALLY_INTERACTS_WITH MALAT1 -> MALAT1 GENE_ENCODES_PROTEIN MALAT1 | {
"steps": [
{
"hop": 1,
"source_node_id": "ATXN2",
"source_node_type": "GENE",
"source_node_label": "ATXN2",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | ATXN2 -> ribonucleoprotein complex -> ILF3 -> ILF3 -> MALAT1 -> MALAT1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATXN2",
"source_db": "UniProt",
"payload": {
"accession": "Q99700",
"sequence": "MRSAAAAPRSPAVATESRRFAAARWPGWRSLQRPARRSGRGGGGAAPGPYPSAAPPPPGPGPPPSRQSSPPSASDCFGSNGNGGGAFRPGSRRLLGLGGPPRPFVVLLLPLASPGAPPAAPTRASPLGARASP... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC393",
"text": "ATXN2 PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "ILF3",
"text": "ILF3 PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex",
"confidence": 1
... | {
"gene_a": "ATXN2",
"gene_b": "MALAT1",
"path_length": 5
} | 0.93874 |
co_path_00134 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from AKT2 to KMT2D through known protein interactions and pathway memberships? | AKT2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AKT1 -> AKT1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II -> KMT2D GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II | {
"steps": [
{
"hop": 1,
"source_node_id": "AKT2",
"source_node_type": "GENE",
"source_node_label": "AKT2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.991,
"edge_source_db": "STRING",
"t... | AKT2 -> AKT1 -> positive regulation of transcription by RNA polymerase II -> KMT2D | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AKT2",
"source_db": "UniProt",
"payload": {
"accession": "P31751",
"sequence": "MNEVSVIKEGWLHKRGEYIKTWRPRYFLLKSDGSFIGYKERPEAPDQTLPPLNNFSVAECQLMKTERPRPNTFVIRCLQWTTVIERTFHVDSPDEREEWMRAIQMVANSLKQRAPGEDPMDYKCGSPSDSSTTE... | [
{
"source_db": "STRING",
"source_id": "AKT1",
"text": "AKT2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AKT1",
"confidence": 0.991
},
{
"source_db": "GO",
"source_id": "GO:0045944",
"text": "AKT1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II",
"co... | {
"gene_a": "AKT2",
"gene_b": "KMT2D",
"path_length": 3
} | 0.709238 |
co_path_00135 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from APC to DNAJC6 through known protein interactions and pathway memberships? | APC GENE_ANNOTATED_WITH_GO_TERM positive regulation of protein catabolic process -> VPS35 GENE_ANNOTATED_WITH_GO_TERM positive regulation of protein catabolic process -> DNAJC6 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH VPS35 | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IGI:MGI",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "GO:004... | APC -> positive regulation of protein catabolic process -> VPS35 -> DNAJC6 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "GO",
"source_id": "GO:0045732",
"text": "APC GENE_ANNOTATED_WITH_GO_TERM positive regulation of protein catabolic process",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "VPS35",
"text": "VPS35 GENE_ANNOTATED_WITH_GO_TERM positive regulation of protein catabo... | {
"gene_a": "APC",
"gene_b": "DNAJC6",
"path_length": 3
} | 0.66503 |
co_path_00136 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from PIK3CA to BRIP1 through known protein interactions and pathway memberships? | PIK3CA GENE_ANNOTATED_WITH_GO_TERM ATP binding -> MLH1 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> MLH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PIK3CA",
"source_node_type": "GENE",
"source_node_label": "PIK3CA",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_no... | PIK3CA -> ATP binding -> MLH1 -> BRIP1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PIK3CA",
"source_db": "UniProt",
"payload": {
"accession": "P42336",
"sequence": "MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVK... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "PIK3CA GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "MLH1",
"text": "MLH1 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "STRING",
... | {
"gene_a": "PIK3CA",
"gene_b": "BRIP1",
"path_length": 3
} | 0.711141 |
co_path_00137 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from BARD1 to CASS4 through known protein interactions and pathway memberships? | Single allele VARIANT_IN_GENE BARD1 -> Single allele VARIANT_IN_GENE APP -> APP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SORL1 -> CASS4 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SORL1 | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | BARD1 -> Single allele -> APP -> SORL1 -> CASS4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BARD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "APP",
"text": "Single allele VARIANT_IN_GENE APP",
"confidence": 1
},
{
"source_db": "STRING",
"source_id"... | {
"gene_a": "BARD1",
"gene_b": "CASS4",
"path_length": 4
} | 0.927881 |
co_path_00138 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from PGR to VPS35 through known protein interactions and pathway memberships? | PGR GENE_ANNOTATED_WITH_GO_TERM negative regulation of gene expression -> VPS35 GENE_ANNOTATED_WITH_GO_TERM negative regulation of gene expression | {
"steps": [
{
"hop": 1,
"source_node_id": "PGR",
"source_node_type": "GENE",
"source_node_label": "PGR",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEP:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | PGR -> negative regulation of gene expression -> VPS35 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PGR",
"source_db": "UniProt",
"payload": {
"accession": "P06401",
"sequence": "MTELKAKGPRAPHVAGGPPSPEVGSPLLCRPAAGPFPGSQTSDTLPEVSAIPISLDGLLFPRPCQGQDPSDEKTQDQQSLSDVEGAYSRAEATRGAGGSSSSPPEKDSGLLDSVLDTLLAPSGPGQSQPSPPACE... | [
{
"source_db": "GO",
"source_id": "GO:0010629",
"text": "PGR GENE_ANNOTATED_WITH_GO_TERM negative regulation of gene expression",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "VPS35",
"text": "VPS35 GENE_ANNOTATED_WITH_GO_TERM negative regulation of gene expression",
"c... | {
"gene_a": "PGR",
"gene_b": "VPS35",
"path_length": 2
} | 0.6 |
co_path_00139 | path_traversal | coding_variant | hard | 5 | What is the shortest molecular path from PRPH to JPH3 through known protein interactions and pathway memberships? | PRPH PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NEFL -> NEFL GENE_ANNOTATED_WITH_GO_TERM axonal transport of mitochondrion -> MAPT GENE_ANNOTATED_WITH_GO_TERM axonal transport of mitochondrion -> MAPT GENE_ANNOTATED_WITH_GO_TERM memory -> JPH3 GENE_ANNOTATED_WITH_GO_TERM memory | {
"steps": [
{
"hop": 1,
"source_node_id": "PRPH",
"source_node_type": "GENE",
"source_node_label": "PRPH",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.902,
"edge_source_db": "STRING",
"t... | PRPH -> NEFL -> axonal transport of mitochondrion -> MAPT -> memory -> JPH3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PRPH",
"source_db": "UniProt",
"payload": {
"accession": "P41219",
"sequence": "MSHHPSGLRAGFSSTSYRRTFGPPPSLSPGAFSYSSSSRFSSSRLLGSASPSSSVRLGSFRSPRAGAGALLRLPSERLDFSMAEALNQEFLATRSNEKQELQELNDRFANFIEKVRFLEQQNAALRGELSQARG... | [
{
"source_db": "STRING",
"source_id": "NEFL",
"text": "PRPH PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NEFL",
"confidence": 0.902
},
{
"source_db": "GO",
"source_id": "GO:0019896",
"text": "NEFL GENE_ANNOTATED_WITH_GO_TERM axonal transport of mitochondrion",
"confidence": 0.6
},
{
... | {
"gene_a": "PRPH",
"gene_b": "JPH3",
"path_length": 5
} | 0.650972 |
co_path_00140 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from SPTLC1 to AR through known protein interactions and pathway memberships? | SPTLC1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of lipophagy -> HTT GENE_ANNOTATED_WITH_GO_TERM positive regulation of lipophagy -> HTT GENE_ANNOTATED_WITH_GO_TERM negative regulation of extrinsic apoptotic signaling pathway -> AR GENE_ANNOTATED_WITH_GO_TERM negative regulation of extrinsic apoptotic signaling p... | {
"steps": [
{
"hop": 1,
"source_node_id": "SPTLC1",
"source_node_type": "GENE",
"source_node_label": "SPTLC1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:MGI",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | SPTLC1 -> positive regulation of lipophagy -> HTT -> negative regulation of extrinsic apoptotic signaling pathway -> AR | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SPTLC1",
"source_db": "UniProt",
"payload": {
"accession": "O15269",
"sequence": "MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEELIEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGT... | [
{
"source_db": "GO",
"source_id": "GO:1904504",
"text": "SPTLC1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of lipophagy",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "HTT",
"text": "HTT GENE_ANNOTATED_WITH_GO_TERM positive regulation of lipophagy",
"confidence": 0... | {
"gene_a": "SPTLC1",
"gene_b": "AR",
"path_length": 4
} | 0.6 |
co_path_00141 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from PSEN2 to CTNNB1 through known protein interactions and pathway memberships? | PSEN2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PSEN1 -> PSEN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PSEN2",
"source_node_type": "GENE",
"source_node_label": "PSEN2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | PSEN2 -> PSEN1 -> CTNNB1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PSEN2",
"source_db": "UniProt",
"payload": {
"accession": "P49810",
"sequence": "MLTFMASDSEEEVCDERTSLMSAESPTPRSCQEGRQGPEDGENTAQWRSQENEEDGEEDPDRYVCSGVPGRPPGLEEELTLKYGAKHVIMLFVPVTLCMIVVVATIKSVRFYTEKNGQLIYTPFTEDTPSVGQ... | [
{
"source_db": "STRING",
"source_id": "PSEN1",
"text": "PSEN2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PSEN1",
"confidence": 0.999
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "PSEN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.999
}
] | {
"gene_a": "PSEN2",
"gene_b": "CTNNB1",
"path_length": 2
} | 0.999 |
co_path_00142 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from BNIP3 to CHEK2 through known protein interactions and pathway memberships? | BNIP3 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> CHEK2 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity | {
"steps": [
{
"hop": 1,
"source_node_id": "BNIP3",
"source_node_type": "GENE",
"source_node_label": "BNIP3",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | BNIP3 -> protein homodimerization activity -> CHEK2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BNIP3",
"source_db": "UniProt",
"payload": {
"accession": "Q12983",
"sequence": "MSQNGAPGMQEESLQGSWVELHFSNNGNGGSVPASVSIYNGDMEKILLDAQHESGRSSSKSSHCDSPPRSQTPQDTNRASETDTHSIGEKNSSQSEEDDIERRKEVESILKKNSDWIWDWSSRPENIPPKEFL... | [
{
"source_db": "GO",
"source_id": "GO:0042803",
"text": "BNIP3 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CHEK2",
"text": "CHEK2 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidenc... | {
"gene_a": "BNIP3",
"gene_b": "CHEK2",
"path_length": 2
} | 0.6 |
co_path_00143 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from DDX41 to ALK through known protein interactions and pathway memberships? | DDX41 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ALK GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "DDX41",
"source_node_type": "GENE",
"source_node_label": "DDX41",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node... | DDX41 -> ATP binding -> ALK | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "DDX41",
"source_db": "UniProt",
"payload": {
"accession": "Q9UJV9",
"sequence": "MEESEPERKRARTDEVPAGGSRSEAEDEDDEDYVPYVPLRQRRQLLLQKLLQRRRKGAAEEEQQDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLKEKAEARKESAKEKQLKEEEKILESVAEGRALMSVKEMA... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "DDX41 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ALK",
"text": "ALK GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
}
] | {
"gene_a": "DDX41",
"gene_b": "ALK",
"path_length": 2
} | 0.6 |
co_path_00144 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from CCND1 to CREBBP through known protein interactions and pathway memberships? | CCND1 GENE_PARTICIPATES_IN_PATHWAY Estrogen-dependent gene expression -> CREBBP GENE_PARTICIPATES_IN_PATHWAY Estrogen-dependent gene expression | {
"steps": [
{
"hop": 1,
"source_node_id": "CCND1",
"source_node_type": "GENE",
"source_node_label": "CCND1",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_id"... | CCND1 -> Estrogen-dependent gene expression -> CREBBP | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CCND1",
"source_db": "UniProt",
"payload": {
"accession": "P24385",
"sequence": "MEHQLLCCEVETIRRAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIR... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-9018519",
"text": "CCND1 GENE_PARTICIPATES_IN_PATHWAY Estrogen-dependent gene expression",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "CREBBP",
"text": "CREBBP GENE_PARTICIPATES_IN_PATHWAY Estrogen-dependent gene expressi... | {
"gene_a": "CCND1",
"gene_b": "CREBBP",
"path_length": 2
} | 1 |
co_path_00145 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from PPP1R1B to ANXA11 through known protein interactions and pathway memberships? | PPP1R1B GENE_ANNOTATED_WITH_GO_TERM protein kinase inhibitor activity -> SNCA GENE_ANNOTATED_WITH_GO_TERM protein kinase inhibitor activity -> SNCA GENE_ANNOTATED_WITH_GO_TERM calcium ion binding -> ANXA11 GENE_ANNOTATED_WITH_GO_TERM calcium ion binding | {
"steps": [
{
"hop": 1,
"source_node_id": "PPP1R1B",
"source_node_type": "GENE",
"source_node_label": "PPP1R1B",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_nod... | PPP1R1B -> protein kinase inhibitor activity -> SNCA -> calcium ion binding -> ANXA11 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PPP1R1B",
"source_db": "UniProt",
"payload": {
"accession": "Q9UD71",
"sequence": "MDPKDRKKIQFSVPAPPSQLDPRQVEMIRRRRPTPAMLFRLSEHSSPEEEASPHQRASGEGHHLKSKRPNPCAYTPPSLKAVQRIAESHLQSISNLNENQASEEEDELGELRELGYPREEDEEEEEDDEEE... | [
{
"source_db": "GO",
"source_id": "GO:0004860",
"text": "PPP1R1B GENE_ANNOTATED_WITH_GO_TERM protein kinase inhibitor activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "SNCA",
"text": "SNCA GENE_ANNOTATED_WITH_GO_TERM protein kinase inhibitor activity",
"confidenc... | {
"gene_a": "PPP1R1B",
"gene_b": "ANXA11",
"path_length": 4
} | 0.6 |
co_path_00146 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from CASP3 to FIG4 through known protein interactions and pathway memberships? | CASP3 GENE_ANNOTATED_WITH_GO_TERM response to ethanol -> SOD1 GENE_ANNOTATED_WITH_GO_TERM response to ethanol -> ALS2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SOD1 -> ALS2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FIG4 | {
"steps": [
{
"hop": 1,
"source_node_id": "CASP3",
"source_node_type": "GENE",
"source_node_label": "CASP3",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:Ensembl",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | CASP3 -> response to ethanol -> SOD1 -> ALS2 -> FIG4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CASP3",
"source_db": "UniProt",
"payload": {
"accession": "P42574",
"sequence": "MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGP... | [
{
"source_db": "GO",
"source_id": "GO:0045471",
"text": "CASP3 GENE_ANNOTATED_WITH_GO_TERM response to ethanol",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "SOD1",
"text": "SOD1 GENE_ANNOTATED_WITH_GO_TERM response to ethanol",
"confidence": 0.6
},
{
"source_d... | {
"gene_a": "CASP3",
"gene_b": "FIG4",
"path_length": 4
} | 0.723452 |
co_path_00147 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from NF1 to CBL through known protein interactions and pathway memberships? | NF1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of apoptotic process -> ABL1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of apoptotic process -> ABL1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CBL | {
"steps": [
{
"hop": 1,
"source_node_id": "NF1",
"source_node_type": "GENE",
"source_node_label": "NF1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "ISS:HGNC-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "G... | NF1 -> positive regulation of apoptotic process -> ABL1 -> CBL | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NF1",
"source_db": "UniProt",
"payload": {
"accession": "P21359",
"sequence": "MAAHRPVEWVQAVVSRFDEQLPIKTGQQNTHTKVSTEHNKECLINISKYKFSLVISGLTTILKNVNNMRIFGEAAEKNLYLSQLIILDTLEKCLAGQPKDTMRLDETMLVKQLLPEICHFLHTCREGNQHAAELR... | [
{
"source_db": "GO",
"source_id": "GO:0043065",
"text": "NF1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of apoptotic process",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ABL1",
"text": "ABL1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of apoptotic process",
... | {
"gene_a": "NF1",
"gene_b": "CBL",
"path_length": 3
} | 0.710429 |
co_path_00148 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from CEBPA to AURKA through known protein interactions and pathway memberships? | CEBPA GENE_ANNOTATED_WITH_GO_TERM protein heterodimerization activity -> AURKA GENE_ANNOTATED_WITH_GO_TERM protein heterodimerization activity | {
"steps": [
{
"hop": 1,
"source_node_id": "CEBPA",
"source_node_type": "GENE",
"source_node_label": "CEBPA",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:Ensembl",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | CEBPA -> protein heterodimerization activity -> AURKA | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CEBPA",
"source_db": "UniProt",
"payload": {
"accession": "P49715",
"sequence": "MESADFYEAEPRPPMSSHLQSPPHAPSSAAFGFPRGAGPAQPPAPPAAPEPLGGICEHETSIDISAYIDPAAFNDEFLADLFQHSRQQEKAKAAVGPTGGGGGGDFDYPGAPAGPGGAVMPGGAHGPPPGYGC... | [
{
"source_db": "GO",
"source_id": "GO:0046982",
"text": "CEBPA GENE_ANNOTATED_WITH_GO_TERM protein heterodimerization activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "AURKA",
"text": "AURKA GENE_ANNOTATED_WITH_GO_TERM protein heterodimerization activity",
"confi... | {
"gene_a": "CEBPA",
"gene_b": "AURKA",
"path_length": 2
} | 0.6 |
co_path_00149 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from APH1B to ETV4 through known protein interactions and pathway memberships? | APH1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APP -> APP GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II -> ETV4 GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II | {
"steps": [
{
"hop": 1,
"source_node_id": "APH1B",
"source_node_type": "GENE",
"source_node_label": "APH1B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.866,
"edge_source_db": "STRING",
... | APH1B -> APP -> positive regulation of transcription by RNA polymerase II -> ETV4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APH1B",
"source_db": "UniProt",
"payload": {
"accession": "Q8WW43",
"sequence": "MTAAVFFGCAFIAFGPALALYVFTIATEPLRIIFLIAGAFFWLVSLLISSLVWFMARVIIDNKDGPTQKYLLIFGAFVSVYIQEMFRFAYYKLLKKASEGLKSINPGETAPSMRLLAYVSGLGFGIMSGVFSF... | [
{
"source_db": "STRING",
"source_id": "APP",
"text": "APH1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APP",
"confidence": 0.866
},
{
"source_db": "GO",
"source_id": "GO:0045944",
"text": "APP GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II",
"conf... | {
"gene_a": "APH1B",
"gene_b": "ETV4",
"path_length": 3
} | 0.678068 |
co_path_00150 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from CD274 to STK11 through known protein interactions and pathway memberships? | CD274 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH STAT3 -> FLT3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH STAT3 -> FLT3 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> STK11 GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "CD274",
"source_node_type": "GENE",
"source_node_label": "CD274",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.992,
"edge_source_db": "STRING",
... | CD274 -> STAT3 -> FLT3 -> ATP binding -> STK11 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD274",
"source_db": "UniProt",
"payload": {
"accession": "Q9NZQ7",
"sequence": "MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP... | [
{
"source_db": "STRING",
"source_id": "STAT3",
"text": "CD274 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH STAT3",
"confidence": 0.992
},
{
"source_db": "STRING",
"source_id": "FLT3",
"text": "FLT3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH STAT3",
"confidence": 0.971
},
{
"source_db":... | {
"gene_a": "CD274",
"gene_b": "STK11",
"path_length": 4
} | 0.767376 |
co_path_00151 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ALB to BCL11B through known protein interactions and pathway memberships? | ACE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ALB -> ACE GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BCL11B GENE_ANNOTATED_WITH_GO_TERM zinc ion binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ALB",
"source_node_type": "GENE",
"source_node_label": "ALB",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.912,
"edge_source_db": "STRING",
"tar... | ALB -> ACE -> zinc ion binding -> BCL11B | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALB",
"source_db": "UniProt",
"payload": {
"accession": "P02768",
"sequence": "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPN... | [
{
"source_db": "STRING",
"source_id": "ACE",
"text": "ACE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ALB",
"confidence": 0.912
},
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "ACE GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO"... | {
"gene_a": "ALB",
"gene_b": "BCL11B",
"path_length": 3
} | 0.689868 |
co_path_00152 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ADM to KMT2C through known protein interactions and pathway memberships? | ACKR3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADM -> Single allele VARIANT_IN_GENE ACKR3 -> Single allele VARIANT_IN_GENE KMT2C | {
"steps": [
{
"hop": 1,
"source_node_id": "ADM",
"source_node_type": "GENE",
"source_node_label": "ADM",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.873,
"edge_source_db": "STRING",
"tar... | ADM -> ACKR3 -> Single allele -> KMT2C | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADM",
"source_db": "UniProt",
"payload": {
"accession": "P35318",
"sequence": "MKLVSVALMYLGSLAFLGADTARLDVASEFRKKWNKWALSRGKRELRMSSSYPTGLADVKAGPAQTLIRPQDMKGASRSPEDSSPDAARIRVKRYRQSMNNFQGLRSFGCRFGTCTVQKLAHQIYQFTDKDKDNV... | [
{
"source_db": "STRING",
"source_id": "ACKR3",
"text": "ACKR3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADM",
"confidence": 0.873
},
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACKR3",
"confidence": 1
},
{
"source_db": "ClinVa... | {
"gene_a": "ADM",
"gene_b": "KMT2C",
"path_length": 3
} | 0.955736 |
co_path_00153 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ASAH1 to MSH2 through known protein interactions and pathway memberships? | ASAH1 GENE_ANNOTATED_WITH_GO_TERM cellular response to tumor necrosis factor -> BRCA1 GENE_ANNOTATED_WITH_GO_TERM cellular response to tumor necrosis factor -> MSH2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "ASAH1",
"source_node_type": "GENE",
"source_node_label": "ASAH1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "ISS:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | ASAH1 -> cellular response to tumor necrosis factor -> BRCA1 -> MSH2 | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ASAH1",
"source_db": "UniProt",
"payload": {
"accession": "Q13510",
"sequence": "MPGRSCVALVLLAAAVSCAVAQHAPPWTEDCRKSTYPPSGPTYRGAVPWYTINLDLPPYKRWHELMLDKAPVLKVIVNSLKNMINTFVPSGKIMQVVDEKLPGLLGNFPGPFEEEMKGIAAVTDIPLGEIISF... | [
{
"source_db": "GO",
"source_id": "GO:0071356",
"text": "ASAH1 GENE_ANNOTATED_WITH_GO_TERM cellular response to tumor necrosis factor",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BRCA1",
"text": "BRCA1 GENE_ANNOTATED_WITH_GO_TERM cellular response to tumor necrosis facto... | {
"gene_a": "ASAH1",
"gene_b": "MSH2",
"path_length": 3
} | 0.709953 |
co_path_00154 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from MSH6 to PALB2 through known protein interactions and pathway memberships? | MSH6 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1 -> BRCA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.996,
"edge_source_db": "STRING",
"t... | MSH6 -> BRCA1 -> PALB2 | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "STRING",
"source_id": "BRCA1",
"text": "MSH6 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1",
"confidence": 0.996
},
{
"source_db": "STRING",
"source_id": "PALB2",
"text": "BRCA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PALB2",
"confidence": 0.999
}
] | {
"gene_a": "MSH6",
"gene_b": "PALB2",
"path_length": 2
} | 0.997499 |
co_path_00155 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from ATP6V1B2 to C9orf72 through known protein interactions and pathway memberships? | ATP6V1B2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ATP6V1A -> ATP6V1A GENE_ANNOTATED_WITH_GO_TERM lysosomal lumen acidification -> GRN GENE_ANNOTATED_WITH_GO_TERM lysosomal lumen acidification -> GRN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH C9orf72 | {
"steps": [
{
"hop": 1,
"source_node_id": "ATP6V1B2",
"source_node_type": "GENE",
"source_node_label": "ATP6V1B2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | ATP6V1B2 -> ATP6V1A -> lysosomal lumen acidification -> GRN -> C9orf72 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATP6V1B2",
"source_db": "UniProt",
"payload": {
"accession": "P21281",
"sequence": "MALRAMRGIVNGAAPELPVPTGGPAVGAREQALAVSRNYLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGR... | [
{
"source_db": "STRING",
"source_id": "ATP6V1A",
"text": "ATP6V1B2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ATP6V1A",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0007042",
"text": "ATP6V1A GENE_ANNOTATED_WITH_GO_TERM lysosomal lumen acidification",
"confidence": 0.6
... | {
"gene_a": "ATP6V1B2",
"gene_b": "C9orf72",
"path_length": 4
} | 0.751533 |
co_path_00156 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from VAPB to ADAM10 through known protein interactions and pathway memberships? | VAPB GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> ADAM10 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity | {
"steps": [
{
"hop": 1,
"source_node_id": "VAPB",
"source_node_type": "GENE",
"source_node_label": "VAPB",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IPI:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | VAPB -> protein homodimerization activity -> ADAM10 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "VAPB",
"source_db": "UniProt",
"payload": {
"accession": "O95292",
"sequence": "MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKPHD... | [
{
"source_db": "GO",
"source_id": "GO:0042803",
"text": "VAPB GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ADAM10",
"text": "ADAM10 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confiden... | {
"gene_a": "VAPB",
"gene_b": "ADAM10",
"path_length": 2
} | 0.6 |
co_path_00157 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from BRCA2 to PPP1R1B through known protein interactions and pathway memberships? | BRCA2 GENE_ANNOTATED_WITH_GO_TERM single-stranded DNA binding -> MAPT GENE_ANNOTATED_WITH_GO_TERM single-stranded DNA binding -> MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK5 -> PPP1R1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK5 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | BRCA2 -> single-stranded DNA binding -> MAPT -> CDK5 -> PPP1R1B | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "GO",
"source_id": "GO:0003697",
"text": "BRCA2 GENE_ANNOTATED_WITH_GO_TERM single-stranded DNA binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "MAPT",
"text": "MAPT GENE_ANNOTATED_WITH_GO_TERM single-stranded DNA binding",
"confidence": 0.6
},
... | {
"gene_a": "BRCA2",
"gene_b": "PPP1R1B",
"path_length": 4
} | 0.769714 |
co_path_00158 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from BRCA1 to FOXA1 through known protein interactions and pathway memberships? | ESR1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1 -> FOXA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ESR1 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | BRCA1 -> ESR1 -> FOXA1 | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "STRING",
"source_id": "ESR1",
"text": "ESR1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1",
"confidence": 0.999
},
{
"source_db": "STRING",
"source_id": "FOXA1",
"text": "FOXA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ESR1",
"confidence": 0.998
}
] | {
"gene_a": "BRCA1",
"gene_b": "FOXA1",
"path_length": 2
} | 0.9985 |
co_path_00159 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from SOX2 to BIRC5 through known protein interactions and pathway memberships? | SOX2 GENE_PARTICIPATES_IN_PATHWAY Interleukin-4 and Interleukin-13 signaling -> BIRC5 GENE_PARTICIPATES_IN_PATHWAY Interleukin-4 and Interleukin-13 signaling | {
"steps": [
{
"hop": 1,
"source_node_id": "SOX2",
"source_node_type": "GENE",
"source_node_label": "SOX2",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_id": ... | SOX2 -> Interleukin-4 and Interleukin-13 signaling -> BIRC5 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SOX2",
"source_db": "UniProt",
"payload": {
"accession": "P48431",
"sequence": "MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTLPGGLLAP... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-6785807",
"text": "SOX2 GENE_PARTICIPATES_IN_PATHWAY Interleukin-4 and Interleukin-13 signaling",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "BIRC5",
"text": "BIRC5 GENE_PARTICIPATES_IN_PATHWAY Interleukin-4 and Interleuk... | {
"gene_a": "SOX2",
"gene_b": "BIRC5",
"path_length": 2
} | 1 |
co_path_00160 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from CD68 to PTEN through known protein interactions and pathway memberships? | CD68 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD4 -> CD4 GENE_PARTICIPATES_IN_PATHWAY Downstream TCR signaling -> PTEN GENE_PARTICIPATES_IN_PATHWAY Downstream TCR signaling | {
"steps": [
{
"hop": 1,
"source_node_id": "CD68",
"source_node_type": "GENE",
"source_node_label": "CD68",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.898,
"edge_source_db": "STRING",
"t... | CD68 -> CD4 -> Downstream TCR signaling -> PTEN | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD68",
"source_db": "UniProt",
"payload": {
"accession": "P34810",
"sequence": "MRLAVLFSGALLGLLAAQGTGNDCPHKKSATLLPSFTVTPTVTESTGTTSHRTTKSHKTTTHRTTTTGTTSHGPTTATHNPTTTSHGNVTVHPTSNSTATSQGPSTATHSPATTSHGNATVHPTSNSTATSPGF... | [
{
"source_db": "STRING",
"source_id": "CD4",
"text": "CD68 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD4",
"confidence": 0.898
},
{
"source_db": "Reactome",
"source_id": "R-HSA-202424",
"text": "CD4 GENE_PARTICIPATES_IN_PATHWAY Downstream TCR signaling",
"confidence": 1
},
{
"... | {
"gene_a": "CD68",
"gene_b": "PTEN",
"path_length": 3
} | 0.964774 |
co_path_00161 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from SLC18A2 to CDK6 through known protein interactions and pathway memberships? | SLC18A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SNCA -> SNCA GENE_ANNOTATED_WITH_GO_TERM negative regulation of transcription by RNA polymerase II -> CCND1 GENE_ANNOTATED_WITH_GO_TERM negative regulation of transcription by RNA polymerase II -> CCND1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK6 | {
"steps": [
{
"hop": 1,
"source_node_id": "SLC18A2",
"source_node_type": "GENE",
"source_node_label": "SLC18A2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.979,
"edge_source_db": "STRING",
... | SLC18A2 -> SNCA -> negative regulation of transcription by RNA polymerase II -> CCND1 -> CDK6 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SLC18A2",
"source_db": "UniProt",
"payload": {
"accession": "Q05940",
"sequence": "MALSELALVRWLQESRRSRKLILFIVFLALLLDNMLLTVVVPIIPSYLYSIKHEKNATEIQTARPVHTASISDSFQSIFSYYDNSTMVTGNATRDLTLHQTATQHMVTNASAVPSDCPSEDKDLLNENVQV... | [
{
"source_db": "STRING",
"source_id": "SNCA",
"text": "SLC18A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SNCA",
"confidence": 0.979
},
{
"source_db": "GO",
"source_id": "GO:0000122",
"text": "SNCA GENE_ANNOTATED_WITH_GO_TERM negative regulation of transcription by RNA polymerase II",
... | {
"gene_a": "SLC18A2",
"gene_b": "CDK6",
"path_length": 4
} | 0.770305 |
co_path_00162 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from MSH2 to PFN1 through known protein interactions and pathway memberships? | MSH2 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ACTB GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ACTB PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PFN1 | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | MSH2 -> ATP binding -> ACTB -> PFN1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "MSH2 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ACTB",
"text": "ACTB GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "STRING",
... | {
"gene_a": "MSH2",
"gene_b": "PFN1",
"path_length": 3
} | 0.711141 |
co_path_00163 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from BST1 to SLC18A2 through known protein interactions and pathway memberships? | BST1 GENE_ANNOTATED_WITH_GO_TERM regulation of calcium-mediated signaling -> MAPT GENE_ANNOTATED_WITH_GO_TERM regulation of calcium-mediated signaling -> MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SNCA -> SLC18A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SNCA | {
"steps": [
{
"hop": 1,
"source_node_id": "BST1",
"source_node_type": "GENE",
"source_node_label": "BST1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IMP:ParkinsonsUK-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_no... | BST1 -> regulation of calcium-mediated signaling -> MAPT -> SNCA -> SLC18A2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BST1",
"source_db": "UniProt",
"payload": {
"accession": "Q10588",
"sequence": "MAAQGCAASRLLQLLLQLLLLLLLLAAGGARARWRGEGTSAHLRDIFLGRCAEYRALLSPEQRNKNCTAIWEAFKVALDKDPCSVLPSDYDLFINLSRHSIPRDKSLFWENSHLLVNSFADNTRRFMPLSDVLY... | [
{
"source_db": "GO",
"source_id": "GO:0050848",
"text": "BST1 GENE_ANNOTATED_WITH_GO_TERM regulation of calcium-mediated signaling",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "MAPT",
"text": "MAPT GENE_ANNOTATED_WITH_GO_TERM regulation of calcium-mediated signaling",
... | {
"gene_a": "BST1",
"gene_b": "SLC18A2",
"path_length": 4
} | 0.769339 |
co_path_00164 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from NOTCH1 to HGF through known protein interactions and pathway memberships? | NOTCH1 GENE_ANNOTATED_WITH_GO_TERM epithelial to mesenchymal transition -> HGF GENE_ANNOTATED_WITH_GO_TERM epithelial to mesenchymal transition | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IMP:BHF-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | NOTCH1 -> epithelial to mesenchymal transition -> HGF | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "GO",
"source_id": "GO:0001837",
"text": "NOTCH1 GENE_ANNOTATED_WITH_GO_TERM epithelial to mesenchymal transition",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "HGF",
"text": "HGF GENE_ANNOTATED_WITH_GO_TERM epithelial to mesenchymal transition",
"confid... | {
"gene_a": "NOTCH1",
"gene_b": "HGF",
"path_length": 2
} | 0.6 |
co_path_00165 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from BRAF to APP through known protein interactions and pathway memberships? | BRAF GENE_ANNOTATED_WITH_GO_TERM positive regulation of ERK1 and ERK2 cascade -> APP GENE_ANNOTATED_WITH_GO_TERM positive regulation of ERK1 and ERK2 cascade | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:BHF-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | BRAF -> positive regulation of ERK1 and ERK2 cascade -> APP | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRAF",
"source_db": "UniProt",
"payload": {
"accession": "P15056",
"sequence": "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSS... | [
{
"source_db": "GO",
"source_id": "GO:0070374",
"text": "BRAF GENE_ANNOTATED_WITH_GO_TERM positive regulation of ERK1 and ERK2 cascade",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "APP",
"text": "APP GENE_ANNOTATED_WITH_GO_TERM positive regulation of ERK1 and ERK2 cascade... | {
"gene_a": "BRAF",
"gene_b": "APP",
"path_length": 2
} | 0.6 |
co_path_00166 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from AKAP11 to ABL2 through known protein interactions and pathway memberships? | AKAP11 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GSK3B -> MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GSK3B -> MAPT GENE_ANNOTATED_WITH_GO_TERM regulation of autophagy -> ABL2 GENE_ANNOTATED_WITH_GO_TERM regulation of autophagy | {
"steps": [
{
"hop": 1,
"source_node_id": "AKAP11",
"source_node_type": "GENE",
"source_node_label": "AKAP11",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.85,
"edge_source_db": "STRING",
... | AKAP11 -> GSK3B -> MAPT -> regulation of autophagy -> ABL2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AKAP11",
"source_db": "UniProt",
"payload": {
"accession": "Q9UKA4",
"sequence": "MATFRNNHMKTKASVRKSFSEDVFQSVKSLLQSQKELCSVTAEDCLQQDEHANLTEVTFLGFNEETDAAHIQDLAAVSLELPDILNSLHFCSLNENEIICMKNINKPLDISSDPLNQSHPSGMLCVMRVSPT... | [
{
"source_db": "STRING",
"source_id": "GSK3B",
"text": "AKAP11 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GSK3B",
"confidence": 0.85
},
{
"source_db": "STRING",
"source_id": "MAPT",
"text": "MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GSK3B",
"confidence": 0.999
},
{
"source_db":... | {
"gene_a": "AKAP11",
"gene_b": "ABL2",
"path_length": 4
} | 0.74357 |
co_path_00167 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from PRKN to BCL2 through known protein interactions and pathway memberships? | PRKN GENE_ANNOTATED_WITH_GO_TERM ubiquitin protein ligase binding -> BCL2 GENE_ANNOTATED_WITH_GO_TERM ubiquitin protein ligase binding | {
"steps": [
{
"hop": 1,
"source_node_id": "PRKN",
"source_node_type": "GENE",
"source_node_label": "PRKN",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IMP:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | PRKN -> ubiquitin protein ligase binding -> BCL2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PRKN",
"source_db": "UniProt",
"payload": {
"accession": "O60260",
"sequence": "MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQSIVHIVQRPWRKGQEMNATGGDDPRNAAGGCEREPQSLTRVDLSSSVLPGDSVGLAVILHTDSRKDSPPA... | [
{
"source_db": "GO",
"source_id": "GO:0031625",
"text": "PRKN GENE_ANNOTATED_WITH_GO_TERM ubiquitin protein ligase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BCL2",
"text": "BCL2 GENE_ANNOTATED_WITH_GO_TERM ubiquitin protein ligase binding",
"confidence": 0... | {
"gene_a": "PRKN",
"gene_b": "BCL2",
"path_length": 2
} | 0.6 |
co_path_00168 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from APOE to TP53 through known protein interactions and pathway memberships? | APOE GENE_ANNOTATED_WITH_GO_TERM positive regulation of DNA-templated transcription -> TP53 GENE_ANNOTATED_WITH_GO_TERM positive regulation of DNA-templated transcription | {
"steps": [
{
"hop": 1,
"source_node_id": "APOE",
"source_node_type": "GENE",
"source_node_label": "APOE",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IMP:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | APOE -> positive regulation of DNA-templated transcription -> TP53 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APOE",
"source_db": "UniProt",
"payload": {
"accession": "P02649",
"sequence": "MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLV... | [
{
"source_db": "GO",
"source_id": "GO:0045893",
"text": "APOE GENE_ANNOTATED_WITH_GO_TERM positive regulation of DNA-templated transcription",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "TP53",
"text": "TP53 GENE_ANNOTATED_WITH_GO_TERM positive regulation of DNA-templated... | {
"gene_a": "APOE",
"gene_b": "TP53",
"path_length": 2
} | 0.6 |
co_path_00169 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from BIRC5 to FLT3 through known protein interactions and pathway memberships? | BIRC5 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation -> FLT3 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "BIRC5",
"source_node_type": "GENE",
"source_node_label": "BIRC5",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | BIRC5 -> positive regulation of cell population proliferation -> FLT3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BIRC5",
"source_db": "UniProt",
"payload": {
"accession": "O15392",
"sequence": "MGAPTLPPAWQPFLKDHRISTFKNWPFLEGCACTPERMAEAGFIHCPTENEPDLAQCFFCFKELEGWEPDDDPIEEHKKHSSGCAFLSVKKQFEELTLGEFLKLDRERAKNKIAKETNNKKKEFEETAKKVRR... | [
{
"source_db": "GO",
"source_id": "GO:0008284",
"text": "BIRC5 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "FLT3",
"text": "FLT3 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell popul... | {
"gene_a": "BIRC5",
"gene_b": "FLT3",
"path_length": 2
} | 0.6 |
co_path_00170 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from FAT4 to ADM through known protein interactions and pathway memberships? | FAT4 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_PARTICIPATES_IN_PATHWAY High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells -> ADM GENE_PARTICIPATES_IN_PATHWAY High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelia... | {
"steps": [
{
"hop": 1,
"source_node_id": "FAT4",
"source_node_type": "GENE",
"source_node_label": "FAT4",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.784,
"edge_source_db": "STRING",
"t... | FAT4 -> CTNNB1 -> High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells -> ADM | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FAT4",
"source_db": "UniProt",
"payload": {
"accession": "Q6V0I7",
"sequence": "MDLAPDRATGRPWLPLHTLSVSQLLRVFWLLSLLPGQAWVHGAEPRQVFQVLEEQPPGTLVGTIQTRPGFTYRLSESHALFAINSSTGALYTTSTIDRESLPSDVINLVVLSSAPTYPTEVRVLVRDLNDNAPV... | [
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "FAT4 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.784
},
{
"source_db": "Reactome",
"source_id": "R-HSA-9856530",
"text": "CTNNB1 GENE_PARTICIPATES_IN_PATHWAY High laminar flow shear stress activates signaling ... | {
"gene_a": "FAT4",
"gene_b": "ADM",
"path_length": 3
} | 0.922087 |
co_path_00171 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ABL2 to BLM through known protein interactions and pathway memberships? | ABL2 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> BLM GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL2",
"source_node_type": "GENE",
"source_node_label": "ABL2",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | ABL2 -> ATP binding -> BLM | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL2",
"source_db": "UniProt",
"payload": {
"accession": "P42684",
"sequence": "MGQQVGRVGEAPGLQQPQPRGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHDHFASCVEDGFEGDKTGGSSPEALHRPYGCDVEPQALNEAIRWSSKENLLGATESDPNLFVALYDFVASGDNTLSITKGEKL... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "ABL2 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BLM",
"text": "BLM GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
}
] | {
"gene_a": "ABL2",
"gene_b": "BLM",
"path_length": 2
} | 0.6 |
co_path_00172 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from ACE to ADRB1 through known protein interactions and pathway memberships? | ACE GENE_ANNOTATED_WITH_GO_TERM endopeptidase activity -> FAP GENE_ANNOTATED_WITH_GO_TERM endopeptidase activity -> FAP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GCG -> ADRB1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GCG | {
"steps": [
{
"hop": 1,
"source_node_id": "ACE",
"source_node_type": "GENE",
"source_node_label": "ACE",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | ACE -> endopeptidase activity -> FAP -> GCG -> ADRB1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACE",
"source_db": "UniProt",
"payload": {
"accession": "P12821",
"sequence": "MGAASGRRGPGLLLPLPLLLLLPPQPALALDPGLQPGNFSADEAGAQLFAQSYNSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQNFTDPQLRRIIGAVRTLGSANLPLA... | [
{
"source_db": "GO",
"source_id": "GO:0004175",
"text": "ACE GENE_ANNOTATED_WITH_GO_TERM endopeptidase activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "FAP",
"text": "FAP GENE_ANNOTATED_WITH_GO_TERM endopeptidase activity",
"confidence": 0.6
},
{
"source... | {
"gene_a": "ACE",
"gene_b": "ADRB1",
"path_length": 4
} | 0.706603 |
co_path_00173 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ALK to HTT through known protein interactions and pathway memberships? | ALK GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fusions and activated point mutants -> TP53 GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fusions and activated point mutants -> HTT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "ALK",
"source_node_type": "GENE",
"source_node_label": "ALK",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_id": "R... | ALK -> Signaling by ALK fusions and activated point mutants -> TP53 -> HTT | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALK",
"source_db": "UniProt",
"payload": {
"accession": "Q9UM73",
"sequence": "MGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPLSYSRLQRKSLAVDFVVPSLFRVYARDLLLPPSSSELKAGRPEARGSLALDCAPLLRLLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKL... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-9725370",
"text": "ALK GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fusions and activated point mutants",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "TP53",
"text": "TP53 GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fus... | {
"gene_a": "ALK",
"gene_b": "HTT",
"path_length": 3
} | 0.999333 |
co_path_00174 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from REST to TMPRSS2 through known protein interactions and pathway memberships? | REST GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding -> ERG GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding -> ERG PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TMPRSS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "REST",
"source_node_type": "GENE",
"source_node_label": "REST",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | REST -> RNA polymerase II cis-regulatory region sequence-specific DNA binding -> ERG -> TMPRSS2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "REST",
"source_db": "UniProt",
"payload": {
"accession": "Q13127",
"sequence": "MATQVMGQSSGGGGLFTSSGNIGMALPNDMYDLHDLSKAELAAPQLIMLANVALTGEVNGSCCDYLVGEERQMAELMPVGDNNFSDSEEGEGLEESADIKGEPHGLENMELRSLELSVVEPQPVFEASGAPDIY... | [
{
"source_db": "GO",
"source_id": "GO:0000978",
"text": "REST GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ERG",
"text": "ERG GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II c... | {
"gene_a": "REST",
"gene_b": "TMPRSS2",
"path_length": 3
} | 0.695123 |
co_path_00175 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from BLM to ACHE through known protein interactions and pathway memberships? | BLM GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> ACHE GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity | {
"steps": [
{
"hop": 1,
"source_node_id": "BLM",
"source_node_type": "GENE",
"source_node_label": "BLM",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | BLM -> protein homodimerization activity -> ACHE | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "GO",
"source_id": "GO:0042803",
"text": "BLM GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ACHE",
"text": "ACHE GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": ... | {
"gene_a": "BLM",
"gene_b": "ACHE",
"path_length": 2
} | 0.6 |
co_path_00176 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from CD8A to ALB through known protein interactions and pathway memberships? | CD8A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD4 -> CD4 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> ACE GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> ACE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ALB | {
"steps": [
{
"hop": 1,
"source_node_id": "CD8A",
"source_node_type": "GENE",
"source_node_label": "CD8A",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | CD8A -> CD4 -> zinc ion binding -> ACE -> ALB | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD8A",
"source_db": "UniProt",
"payload": {
"accession": "P01732",
"sequence": "MALPVTALLLPLALLLHAARPSQFRVSPLDRTWNLGETVELKCQVLLSNPTSGCSWLFQPRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLGDTFVLTLSDFRRENEGYYFCSALSNSIMYFSHFVPVFLP... | [
{
"source_db": "STRING",
"source_id": "CD4",
"text": "CD8A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD4",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "CD4 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO... | {
"gene_a": "CD8A",
"gene_b": "ALB",
"path_length": 4
} | 0.756773 |
co_path_00177 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from NEK1 to CD8A through known protein interactions and pathway memberships? | NEK1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH VAPB -> VAPB GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> CD4 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> CD4 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD8A | {
"steps": [
{
"hop": 1,
"source_node_id": "NEK1",
"source_node_type": "GENE",
"source_node_label": "NEK1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.717,
"edge_source_db": "STRING",
"t... | NEK1 -> VAPB -> protein homodimerization activity -> CD4 -> CD8A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NEK1",
"source_db": "UniProt",
"payload": {
"accession": "Q96PY6",
"sequence": "MEKYVRLQKIGEGSFGKAILVKSTEDGRQYVIKEINISRMSSKEREESRREVAVLANMKHPNIVQYRESFEENGSLYIVMDYCEGGDLFKRINAQKGVLFQEDQILDWFVQICLALKHVHDRKILHRDIKSQNI... | [
{
"source_db": "STRING",
"source_id": "VAPB",
"text": "NEK1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH VAPB",
"confidence": 0.717
},
{
"source_db": "GO",
"source_id": "GO:0042803",
"text": "VAPB GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": 0.6
},
{
... | {
"gene_a": "NEK1",
"gene_b": "CD8A",
"path_length": 4
} | 0.712602 |
co_path_00178 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from RXRA to ERG through known protein interactions and pathway memberships? | RXRA GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding -> ERG GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding | {
"steps": [
{
"hop": 1,
"source_node_id": "RXRA",
"source_node_type": "GENE",
"source_node_label": "RXRA",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:MGI",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "GO:0... | RXRA -> RNA polymerase II cis-regulatory region sequence-specific DNA binding -> ERG | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RXRA",
"source_db": "UniProt",
"payload": {
"accession": "P19793",
"sequence": "MDTKHFLPLDFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHI... | [
{
"source_db": "GO",
"source_id": "GO:0000978",
"text": "RXRA GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ERG",
"text": "ERG GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II c... | {
"gene_a": "RXRA",
"gene_b": "ERG",
"path_length": 2
} | 0.6 |
co_path_00179 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from CD8A to CDC25B through known protein interactions and pathway memberships? | CD8A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD4 -> CD4 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> CDC25B GENE_ANNOTATED_WITH_GO_TERM protein kinase binding | {
"steps": [
{
"hop": 1,
"source_node_id": "CD8A",
"source_node_type": "GENE",
"source_node_label": "CD8A",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | CD8A -> CD4 -> protein kinase binding -> CDC25B | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD8A",
"source_db": "UniProt",
"payload": {
"accession": "P01732",
"sequence": "MALPVTALLLPLALLLHAARPSQFRVSPLDRTWNLGETVELKCQVLLSNPTSGCSWLFQPRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLGDTFVLTLSDFRRENEGYYFCSALSNSIMYFSHFVPVFLP... | [
{
"source_db": "STRING",
"source_id": "CD4",
"text": "CD8A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD4",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "CD4 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source_db... | {
"gene_a": "CD8A",
"gene_b": "CDC25B",
"path_length": 3
} | 0.711141 |
co_path_00180 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from NOTCH1 to KRAS through known protein interactions and pathway memberships? | NOTCH1 GENE_ANNOTATED_WITH_GO_TERM cardiac muscle cell proliferation -> KRAS GENE_ANNOTATED_WITH_GO_TERM cardiac muscle cell proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:Ensembl",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | NOTCH1 -> cardiac muscle cell proliferation -> KRAS | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "GO",
"source_id": "GO:0060038",
"text": "NOTCH1 GENE_ANNOTATED_WITH_GO_TERM cardiac muscle cell proliferation",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "KRAS",
"text": "KRAS GENE_ANNOTATED_WITH_GO_TERM cardiac muscle cell proliferation",
"confidence... | {
"gene_a": "NOTCH1",
"gene_b": "KRAS",
"path_length": 2
} | 0.6 |
co_path_00181 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from CDK4 to AKAP11 through known protein interactions and pathway memberships? | CDK4 GENE_ANNOTATED_WITH_GO_TERM regulation of gene expression -> PSEN1 GENE_ANNOTATED_WITH_GO_TERM regulation of gene expression -> PSEN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GSK3B -> AKAP11 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GSK3B | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK4",
"source_node_type": "GENE",
"source_node_label": "CDK4",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IMP:BHF-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | CDK4 -> regulation of gene expression -> PSEN1 -> GSK3B -> AKAP11 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK4",
"source_db": "UniProt",
"payload": {
"accession": "P11802",
"sequence": "MATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGGGGGLPISTVREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQFLRGLDFLHAN... | [
{
"source_db": "GO",
"source_id": "GO:0010468",
"text": "CDK4 GENE_ANNOTATED_WITH_GO_TERM regulation of gene expression",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "PSEN1",
"text": "PSEN1 GENE_ANNOTATED_WITH_GO_TERM regulation of gene expression",
"confidence": 0.6
... | {
"gene_a": "CDK4",
"gene_b": "AKAP11",
"path_length": 4
} | 0.742824 |
co_path_00182 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from FLT3 to C9orf72 through known protein interactions and pathway memberships? | FLT3 GENE_ANNOTATED_WITH_GO_TERM regulation of apoptotic process -> TARDBP GENE_ANNOTATED_WITH_GO_TERM regulation of apoptotic process -> C9orf72 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TARDBP | {
"steps": [
{
"hop": 1,
"source_node_id": "FLT3",
"source_node_type": "GENE",
"source_node_label": "FLT3",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | FLT3 -> regulation of apoptotic process -> TARDBP -> C9orf72 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FLT3",
"source_db": "UniProt",
"payload": {
"accession": "P36888",
"sequence": "MPALARDGGQLPLLVVFSAMIFGTITNQDLPVIKCVLINHKNNDSSVGKSSSYPMVSESPEDLGCALRPQSSGTVYEAAAVEVDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMT... | [
{
"source_db": "GO",
"source_id": "GO:0042981",
"text": "FLT3 GENE_ANNOTATED_WITH_GO_TERM regulation of apoptotic process",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "TARDBP",
"text": "TARDBP GENE_ANNOTATED_WITH_GO_TERM regulation of apoptotic process",
"confidence":... | {
"gene_a": "FLT3",
"gene_b": "C9orf72",
"path_length": 3
} | 0.697597 |
co_path_00183 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from PDE10A to PTEN through known protein interactions and pathway memberships? | PDE10A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ENPP1 -> BST1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ENPP1 -> BST1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation -> PTEN GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "PDE10A",
"source_node_type": "GENE",
"source_node_label": "PDE10A",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.929,
"edge_source_db": "STRING",
... | PDE10A -> ENPP1 -> BST1 -> positive regulation of cell population proliferation -> PTEN | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PDE10A",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y233",
"sequence": "MASLEEPLAPRPQGPLPAAGDEPGCGPGKLRPEPRLSAAGGGSAAGPGPAPEWPGRGRAERAAPPRPPLSSAGRPSPAGGPGALSARGGGCGWVAARAPLALAFSSRVPSSSPSFFYFWPPPPPPPPSFLPS... | [
{
"source_db": "STRING",
"source_id": "ENPP1",
"text": "PDE10A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ENPP1",
"confidence": 0.929
},
{
"source_db": "STRING",
"source_id": "BST1",
"text": "BST1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ENPP1",
"confidence": 0.93
},
{
"source_db":... | {
"gene_a": "PDE10A",
"gene_b": "PTEN",
"path_length": 4
} | 0.746793 |
co_path_00184 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from KRAS to APOE through known protein interactions and pathway memberships? | KRAS PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRAF -> BRAF GENE_ANNOTATED_WITH_GO_TERM positive regulation of ERK1 and ERK2 cascade -> APOE GENE_ANNOTATED_WITH_GO_TERM positive regulation of ERK1 and ERK2 cascade | {
"steps": [
{
"hop": 1,
"source_node_id": "KRAS",
"source_node_type": "GENE",
"source_node_label": "KRAS",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | KRAS -> BRAF -> positive regulation of ERK1 and ERK2 cascade -> APOE | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01116",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLA... | [
{
"source_db": "STRING",
"source_id": "BRAF",
"text": "KRAS PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRAF",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0070374",
"text": "BRAF GENE_ANNOTATED_WITH_GO_TERM positive regulation of ERK1 and ERK2 cascade",
"confidence": 0.... | {
"gene_a": "KRAS",
"gene_b": "APOE",
"path_length": 3
} | 0.711141 |
co_path_00185 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from IL17A to CDK1 through known protein interactions and pathway memberships? | IL17A GENE_ANNOTATED_WITH_GO_TERM apoptotic process -> CDK1 GENE_ANNOTATED_WITH_GO_TERM apoptotic process | {
"steps": [
{
"hop": 1,
"source_node_id": "IL17A",
"source_node_type": "GENE",
"source_node_label": "IL17A",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:ProtInc",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | IL17A -> apoptotic process -> CDK1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "IL17A",
"source_db": "UniProt",
"payload": {
"accession": "Q16552",
"sequence": "MTPGKTSLVSLLLLLSLEAIVKAGITIPRNPGCPNSEDKNFPRTVMVNLNIHNRNTNTNPKRSSDYYNRSTSPWNLHRNEDPERYPSVIWEAKCRHLGCINADGNVDYHMNSVPIQQEILVLRREPPHCPNSF... | [
{
"source_db": "GO",
"source_id": "GO:0006915",
"text": "IL17A GENE_ANNOTATED_WITH_GO_TERM apoptotic process",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CDK1",
"text": "CDK1 GENE_ANNOTATED_WITH_GO_TERM apoptotic process",
"confidence": 0.6
}
] | {
"gene_a": "IL17A",
"gene_b": "CDK1",
"path_length": 2
} | 0.6 |
co_path_00186 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from REST to MLH1 through known protein interactions and pathway memberships? | REST GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BLM GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BLM PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "REST",
"source_node_type": "GENE",
"source_node_label": "REST",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | REST -> zinc ion binding -> BLM -> MLH1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "REST",
"source_db": "UniProt",
"payload": {
"accession": "Q13127",
"sequence": "MATQVMGQSSGGGGLFTSSGNIGMALPNDMYDLHDLSKAELAAPQLIMLANVALTGEVNGSCCDYLVGEERQMAELMPVGDNNFSDSEEGEGLEESADIKGEPHGLENMELRSLELSVVEPQPVFEASGAPDIY... | [
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "REST GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BLM",
"text": "BLM GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "STRI... | {
"gene_a": "REST",
"gene_b": "MLH1",
"path_length": 3
} | 0.711141 |
co_path_00187 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from REST to PTEN through known protein interactions and pathway memberships? | REST GENE_ANNOTATED_WITH_GO_TERM cellular response to electrical stimulus -> PTEN GENE_ANNOTATED_WITH_GO_TERM cellular response to electrical stimulus | {
"steps": [
{
"hop": 1,
"source_node_id": "REST",
"source_node_type": "GENE",
"source_node_label": "REST",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IMP:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | REST -> cellular response to electrical stimulus -> PTEN | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "REST",
"source_db": "UniProt",
"payload": {
"accession": "Q13127",
"sequence": "MATQVMGQSSGGGGLFTSSGNIGMALPNDMYDLHDLSKAELAAPQLIMLANVALTGEVNGSCCDYLVGEERQMAELMPVGDNNFSDSEEGEGLEESADIKGEPHGLENMELRSLELSVVEPQPVFEASGAPDIY... | [
{
"source_db": "GO",
"source_id": "GO:0071257",
"text": "REST GENE_ANNOTATED_WITH_GO_TERM cellular response to electrical stimulus",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "PTEN",
"text": "PTEN GENE_ANNOTATED_WITH_GO_TERM cellular response to electrical stimulus",
... | {
"gene_a": "REST",
"gene_b": "PTEN",
"path_length": 2
} | 0.6 |
co_path_00188 | path_traversal | coding_variant | easy | 3 | What is the shortest molecular path from MAPT to UBQLN2 through known protein interactions and pathway memberships? | MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SNCA -> SNCA PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TARDBP -> UBQLN2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TARDBP | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPT",
"source_node_type": "GENE",
"source_node_label": "MAPT",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.994,
"edge_source_db": "STRING",
"t... | MAPT -> SNCA -> TARDBP -> UBQLN2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPT",
"source_db": "UniProt",
"payload": {
"accession": "P10636",
"sequence": "MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQEPESGKVVQE... | [
{
"source_db": "STRING",
"source_id": "SNCA",
"text": "MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SNCA",
"confidence": 0.994
},
{
"source_db": "STRING",
"source_id": "TARDBP",
"text": "SNCA PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TARDBP",
"confidence": 0.994
},
{
"source_db":... | {
"gene_a": "MAPT",
"gene_b": "UBQLN2",
"path_length": 3
} | 0.985257 |
co_path_00189 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ADAM10 to CDK1 through known protein interactions and pathway memberships? | ADAM10 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APP -> APP GENE_ANNOTATED_WITH_GO_TERM positive regulation of gene expression -> CDK1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of gene expression | {
"steps": [
{
"hop": 1,
"source_node_id": "ADAM10",
"source_node_type": "GENE",
"source_node_label": "ADAM10",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.95,
"edge_source_db": "STRING",
... | ADAM10 -> APP -> positive regulation of gene expression -> CDK1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADAM10",
"source_db": "UniProt",
"payload": {
"accession": "O14672",
"sequence": "MVLLRVLILLLSWAAGMGGQYGNPLNKYIRHYEGLSYNVDSLHQKHQRAKRAVSHEDQFLRLDFHAHGRHFNLRMKRDTSLFSDEFKVETSNKVLDYDTSHIYTGHIYGEEGSFSHGSVIDGRFEGFIQTRG... | [
{
"source_db": "STRING",
"source_id": "APP",
"text": "ADAM10 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APP",
"confidence": 0.95
},
{
"source_db": "GO",
"source_id": "GO:0010628",
"text": "APP GENE_ANNOTATED_WITH_GO_TERM positive regulation of gene expression",
"confidence": 0.6
},
... | {
"gene_a": "ADAM10",
"gene_b": "CDK1",
"path_length": 3
} | 0.699319 |
co_path_00190 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from AFF3 to MLH3 through known protein interactions and pathway memberships? | AFF3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK9 -> CDK12 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK9 -> CDK12 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> MLH3 GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "AFF3",
"source_node_type": "GENE",
"source_node_label": "AFF3",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.947,
"edge_source_db": "STRING",
"t... | AFF3 -> CDK9 -> CDK12 -> ATP binding -> MLH3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFF3",
"source_db": "UniProt",
"payload": {
"accession": "P51826",
"sequence": "MDSFDLALLQEWDLESLCVYEPDRNALRRKERERRNQETQQDDGTFNSSYSLFSEPYKTNKGDELSNRIQNTLGNYDEMKDFLTDRSNQSHLVGVPKPGVPQTPVNKIDEHFVADSRAQNQPSSICSTTTSTPA... | [
{
"source_db": "STRING",
"source_id": "CDK9",
"text": "AFF3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK9",
"confidence": 0.947
},
{
"source_db": "STRING",
"source_id": "CDK12",
"text": "CDK12 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK9",
"confidence": 0.899
},
{
"source_db": "... | {
"gene_a": "AFF3",
"gene_b": "MLH3",
"path_length": 4
} | 0.744052 |
co_path_00191 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from SLC6A2 to NOTCH1 through known protein interactions and pathway memberships? | SLC6A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADRA2A -> ADRA2A GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell migration -> NOTCH1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell migration | {
"steps": [
{
"hop": 1,
"source_node_id": "SLC6A2",
"source_node_type": "GENE",
"source_node_label": "SLC6A2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.802,
"edge_source_db": "STRING",
... | SLC6A2 -> ADRA2A -> positive regulation of cell migration -> NOTCH1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SLC6A2",
"source_db": "UniProt",
"payload": {
"accession": "P23975",
"sequence": "MLLARMNPQVQPENNGADTGPEQPLRARKTAELLVVKERNGVQCLLAPRDGDAQPRETWGKKIDFLLSVVGFAVDLANVWRFPYLCYKNGGGAFLIPYTLFLIIAGMPLFYMELALGQYNREGAATVWKICP... | [
{
"source_db": "STRING",
"source_id": "ADRA2A",
"text": "SLC6A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ADRA2A",
"confidence": 0.802
},
{
"source_db": "GO",
"source_id": "GO:0030335",
"text": "ADRA2A GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell migration",
"confidence": 0... | {
"gene_a": "SLC6A2",
"gene_b": "NOTCH1",
"path_length": 3
} | 0.660935 |
co_path_00192 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from RET to OPTN through known protein interactions and pathway memberships? | RET GENE_ANNOTATED_WITH_GO_TERM ATP binding -> TBK1 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> TBK1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH OPTN | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id"... | RET -> ATP binding -> TBK1 -> OPTN | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RET",
"source_db": "UniProt",
"payload": {
"accession": "P07949",
"sequence": "MAKATSGAAGLRLLLLLLLPLLGKVALGLYFSRDAYWEKLYVDQAAGTPLLYVHALRDAPEEVPSFRLGQHLYGTYRTRLHENNWICIQEDTGLLYLNRSLDHSSWEKLSVRNRGFPLLTVYLKVFLSPTSLREG... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "RET GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "TBK1",
"text": "TBK1 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "STRING",
... | {
"gene_a": "RET",
"gene_b": "OPTN",
"path_length": 3
} | 0.711141 |
co_path_00193 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from CDX2 to ATXN2 through known protein interactions and pathway memberships? | CDX2 GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding -> TARDBP GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding -> TARDBP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ATXN2 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDX2",
"source_node_type": "GENE",
"source_node_label": "CDX2",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:NTNU_SB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | CDX2 -> RNA polymerase II cis-regulatory region sequence-specific DNA binding -> TARDBP -> ATXN2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDX2",
"source_db": "UniProt",
"payload": {
"accession": "Q99626",
"sequence": "MYVSYLLDKDVSMYPSSVRHSGGLNLAPQNFVSPPQYPDYGGYHVAAAAAAAANLDSAQSPGPSWPAAYGAPLREDWNGYAPGGAAAAANAVAHGLNGGSPAAAMGYSSPADYHPHHHPHHHPHHPAAAPSCAS... | [
{
"source_db": "GO",
"source_id": "GO:0000978",
"text": "CDX2 GENE_ANNOTATED_WITH_GO_TERM RNA polymerase II cis-regulatory region sequence-specific DNA binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "TARDBP",
"text": "TARDBP GENE_ANNOTATED_WITH_GO_TERM RNA polymeras... | {
"gene_a": "CDX2",
"gene_b": "ATXN2",
"path_length": 3
} | 0.709477 |
co_path_00194 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from OPTN to BRIP1 through known protein interactions and pathway memberships? | OPTN GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BRCA1 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BRIP1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "OPTN",
"source_node_type": "GENE",
"source_node_label": "OPTN",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | OPTN -> zinc ion binding -> BRCA1 -> BRIP1 | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "OPTN",
"source_db": "UniProt",
"payload": {
"accession": "Q96CV9",
"sequence": "MSHQPLSCLTEKEDSPSESTGNGPPHLAHPNLDTFTPEELLQQMKELLTENHQLKEAMKLNNQAMKGRFEELSAWTEKQKEERQFFEIQSKEAKERLMALSHENEKLKEELGKLKGKSERSSEDPTDDSRLPRA... | [
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "OPTN GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BRCA1",
"text": "BRCA1 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "... | {
"gene_a": "OPTN",
"gene_b": "BRIP1",
"path_length": 3
} | 0.711141 |
co_path_00195 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from PPP1R1B to SNCA through known protein interactions and pathway memberships? | PPP1R1B GENE_ANNOTATED_WITH_GO_TERM protein kinase inhibitor activity -> SNCA GENE_ANNOTATED_WITH_GO_TERM protein kinase inhibitor activity | {
"steps": [
{
"hop": 1,
"source_node_id": "PPP1R1B",
"source_node_type": "GENE",
"source_node_label": "PPP1R1B",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_nod... | PPP1R1B -> protein kinase inhibitor activity -> SNCA | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PPP1R1B",
"source_db": "UniProt",
"payload": {
"accession": "Q9UD71",
"sequence": "MDPKDRKKIQFSVPAPPSQLDPRQVEMIRRRRPTPAMLFRLSEHSSPEEEASPHQRASGEGHHLKSKRPNPCAYTPPSLKAVQRIAESHLQSISNLNENQASEEEDELGELRELGYPREEDEEEEEDDEEE... | [
{
"source_db": "GO",
"source_id": "GO:0004860",
"text": "PPP1R1B GENE_ANNOTATED_WITH_GO_TERM protein kinase inhibitor activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "SNCA",
"text": "SNCA GENE_ANNOTATED_WITH_GO_TERM protein kinase inhibitor activity",
"confidenc... | {
"gene_a": "PPP1R1B",
"gene_b": "SNCA",
"path_length": 2
} | 0.6 |
co_path_00196 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from AURKA to FAT4 through known protein interactions and pathway memberships? | AURKA PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53 -> FAT4 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "AURKA",
"source_node_type": "GENE",
"source_node_label": "AURKA",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
... | AURKA -> TP53 -> FAT4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AURKA",
"source_db": "UniProt",
"payload": {
"accession": "O14965",
"sequence": "MDRSKENCISGPVKATAPVGGPKRVLVTQQFPCQNPLPVNSGQAQRVLCPSNSSQRIPLQAQKLVSSHKPVQNQKQKQLQATSVPHPVSRPLNNTQKSKQPLPSAPENNPEEELASKQKNEESKKRQWALEDF... | [
{
"source_db": "STRING",
"source_id": "TP53",
"text": "AURKA PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53",
"confidence": 0.998
},
{
"source_db": "STRING",
"source_id": "FAT4",
"text": "FAT4 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53",
"confidence": 0.658
}
] | {
"gene_a": "AURKA",
"gene_b": "FAT4",
"path_length": 2
} | 0.81036 |
co_path_00197 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from TARDBP to RAD51D through known protein interactions and pathway memberships? | TARDBP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SNCA -> SNCA GENE_ANNOTATED_WITH_GO_TERM supramolecular fiber organization -> RAD51D GENE_ANNOTATED_WITH_GO_TERM supramolecular fiber organization | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.994,
"edge_source_db": "STRING",
... | TARDBP -> SNCA -> supramolecular fiber organization -> RAD51D | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TARDBP",
"source_db": "UniProt",
"payload": {
"accession": "Q13148",
"sequence": "MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLM... | [
{
"source_db": "STRING",
"source_id": "SNCA",
"text": "TARDBP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SNCA",
"confidence": 0.994
},
{
"source_db": "GO",
"source_id": "GO:0097435",
"text": "SNCA GENE_ANNOTATED_WITH_GO_TERM supramolecular fiber organization",
"confidence": 0.6
},
... | {
"gene_a": "TARDBP",
"gene_b": "RAD51D",
"path_length": 3
} | 0.709953 |
co_path_00198 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from PRKN to CD4 through known protein interactions and pathway memberships? | PRKN GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> CD4 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding | {
"steps": [
{
"hop": 1,
"source_node_id": "PRKN",
"source_node_type": "GENE",
"source_node_label": "PRKN",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IPI:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id":... | PRKN -> protein kinase binding -> CD4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PRKN",
"source_db": "UniProt",
"payload": {
"accession": "O60260",
"sequence": "MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQSIVHIVQRPWRKGQEMNATGGDDPRNAAGGCEREPQSLTRVDLSSSVLPGDSVGLAVILHTDSRKDSPPA... | [
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "PRKN GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CD4",
"text": "CD4 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
}
] | {
"gene_a": "PRKN",
"gene_b": "CD4",
"path_length": 2
} | 0.6 |
co_path_00199 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from IGFBP3 to CASP2 through known protein interactions and pathway memberships? | IGFBP3 GENE_ANNOTATED_WITH_GO_TERM apoptotic process -> CASP2 GENE_ANNOTATED_WITH_GO_TERM apoptotic process | {
"steps": [
{
"hop": 1,
"source_node_id": "IGFBP3",
"source_node_type": "GENE",
"source_node_label": "IGFBP3",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_no... | IGFBP3 -> apoptotic process -> CASP2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "IGFBP3",
"source_db": "UniProt",
"payload": {
"accession": "P17936",
"sequence": "MQRARPTLWAAALTLLVLLRGPPVARAGASSAGLGPVVRCEPCDARALAQCAPPPAVCAELVREPGCGCCLTCALSEGQPCGIYTERCGSGLRCQPSPDEARPLQALLDGRGLCVNASAVSRLRAYLLPAPP... | [
{
"source_db": "GO",
"source_id": "GO:0006915",
"text": "IGFBP3 GENE_ANNOTATED_WITH_GO_TERM apoptotic process",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CASP2",
"text": "CASP2 GENE_ANNOTATED_WITH_GO_TERM apoptotic process",
"confidence": 0.6
}
] | {
"gene_a": "IGFBP3",
"gene_b": "CASP2",
"path_length": 2
} | 0.6 |
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